Modulation of an Individual&#39;s Gut Microbiome to Address Osteoporosis and Bone Disease

ABSTRACT

Various embodiments of the present invention are directed to the field of treating and preventing osteoporosis, with particular embodiments directed to a method of ameliorating, treating, or preventing osteoporosis in a human subject employing tomatidine, xylitol, rapamycin, etc., as well as modifying an individual’s microbiome to reduce the likelihood of osteoporosis.

RELATED APPLICATIONS

This application is a continuation-in-part of U.S. Pat. ApplicationSerial No. 17/893,384, filed on Aug. 23, 2022, which is a continuationof U.S. Pat. Application Serial No. 17/694,775, filed Mar. 15, 2022,which is a continuation-in-part of U.S. Pat. Application Serial No.17/023,736, filed on Sep. 17, 2020 (now U.S. Pat. No. 11,419,903, issuedAug. 23, 2022), which is a continuation-in-part of U.S. Pat. ApplicationSerial No. 17/011,175, filed on Sep. 3, 2020 (now U.S. Pat. No.11,273,187, issuing Mar. 15, 2022), which is a continuation-in-part U.S.Pat. Application Ser. No. 16/722,117, filed Dec. 20, 2019 (now U.S. Pat.No. 10,842,834, issued Nov. 24, 2020), and is a continuation-in-part ofU.S. Pat. Application Ser. No. 16/229,252, filed Dec. 21, 2018 (now U.S.Pat. No. 10,512,661, issued Dec. 24, 2019), which is acontinuation-in-part of U.S. Pat. Application Ser. No. 15/392,173, filedDec. 28, 2016 (now U.S. Pat. No. 10,245,288, issued Apr. 2, 2019), whichis a non-provisional of U.S. Provisional Pat. Application Ser. No.62/275,341, filed on Jan. 6, 2016.

This application is also a continuation-in-part of U.S. Pat. ApplicationSerial No. 16/917,096, filed Jun. 30, 2020 (now U.S. Pat. No.10,940,169, issued Mar. 9, 2021), which is a continuation-in-part ofU.S. Pat. Application Serial No. 16/782,364, filed Feb. 5, 2020 (nowU.S. Pat. No. 10,835,560, issued Nov. 17, 2020), which is acontinuation-in-part of U.S. Pat. Application Serial No. 16/423,375,filed May 28, 2019 (now U.S. Pat. No. 10,555,976, issued Feb. 11, 2020),which is a continuation of U.S. Pat. Application Serial No. 16/160,336,filed Oct. 15, 2018 (now U.S. Pat. No. 10,314,866, issued Jun. 11,2019), which is a continuation of U.S. Pat. Application Serial No.15/403,823, filed Jan. 11, 2017 (now U.S. Pat. No. 10,111,913, issuedOct. 30, 2018), which is a non-provisional of U.S. Provisional Pat.Application Serial No. 62/296,186, filed on Feb. 17, 2016.

This application also is a continuation-in-part application of U.S. Pat.Application Serial No. 15/270,034, filed Sep. 20, 2016 (now U.S. Pat.No. 9,750,802, issued Sep. 5, 2017), which is a continuation-in-partapplication of U.S. Pat. Application Serial No. 14/954,074, filed onNov. 30, 2015 (now issued U.S. Pat. No. 9,457,077, issuing on Oct. 4,2016).

This application is a continuation-in-part of U.S. Pat. ApplicationSerial No. 16/426,346, filed May 30, 2019 (now U.S. Pat. No. 10,716,815,issued Jul. 21, 2020), which is a continuation of U.S. Pat. ApplicationSerial No. 15/639,767, filed Jun. 30, 2017 (now issued U.S. Pat. No.10,314,865, issuing Jun. 11, 2019), which is a continuation-in-part ofU.S. Pat. Application Serial No. 15/437,976, filed Feb. 21, 2017 (nowU.S. Pat. No. 9,730,967, issued Aug. 15, 2017), which is acontinuation-in-part application of U.S. Pat. Application Serial No.15/228,454, filed Aug. 4, 2016 (now U.S. Pat. No. 9,585,920, issued Mar.7, 2017), which is a continuation-in-part application of U.S. Pat.Application Serial No. 14/954,074, filed on Nov. 30, 2015 (now issuedU.S. Pat. No. 9,457,077, issued Oct. 4, 2016).

This application is a continuation-in-part application of U.S. Pat.Application Serial No. 16/776,861, filed Jan. 30, 2020 (now U.S. Pat.No. 10,864,109, issued Dec. 15, 2020), which is a continuation of U.S.Pat. Application Serial No. 16/142,171, filed Sep. 26, 2018 (now U.S.Pat. No. 10,548,761, issued Feb. 4, 2020), which is acontinuation-in-part of U.S. Pat. Application Serial No. 15/395,419,filed Dec. 30, 2016 (now U.S. Pat. No. 10,086,018, issued Oct. 2, 2018),which is a non-provisional of U.S. Provisional Pat. Application SerialNo. 62/274,550, filed on Jan. 4, 2016.

This application is a continuation-in-part of U.S. Pat. ApplicationSerial No. 16/904,056, filed Jun. 17, 2020 (now U.S. Pat. No.11,523,934, issued Dec. 13, 2022), which is a continuation-in-part ofU.S. Pat. Application Serial No. 15/983,250 filed on May 18, 2018 (nowU.S. Pat. No. 10,687,975, issued Jun. 23, 2020), which is acontinuation-in-part of U.S. Pat. Application Serial No. 15/384,716filed on Dec. 20, 2016 (now issued U.S. Pat. No. 9,987,224, issued Jun.5, 2018), which claims priority of U.S. Provisional Pat. ApplicationSerial Nos. 62/387,405, filed on Dec. 24, 2015.

The entire disclosure of the prior applications are considered to bepart of the disclosure of the accompanying application and are herebyincorporated by reference.

FIELD OF THE INVENTION

The present invention is directed to the treating, preventing andreducing the likelihood of osteoporosis, with particular embodimentsdirected to a method employing tomatidine, xylitol, and rapamycin, aswell as modifying an individual’s microbiome to reduce the likelihood ofosteoporosis.

BACKGROUND OF THE INVENTION

Osteoporosis is a metabolic disease that can cause pain and fragilityfractures. It is a degenerative joint disease associated with chronicpain and disability involving articular cartilage breakdown, synovialinflammation, and bone hypertrophy. It is characterized by bone massloss, microarchitectural destruction, decreasing bone mass density,increased possibility of fragility fracture, disruption of bonemicro-architecture, and changes to the amount and variety ofnon-collagenous proteins in the bone. The incidence of senileosteoporosis increases every year, with the incidence of osteoporoticfractures of women in their 50s now at 50%. There are over a millionosteoporotic fractures each year in the USA and osteoporosis has becomea serious worldwide health problem.

The loss of bone mass and microarchitecture deterioration of bone tissueis attributed to various factors, including menopause, aging, andadverse effects of relevant medications. In recent decades, knowledgeregarding the etiological mechanisms underpinning osteoporosisemphasizes that bone cellular homeostasis, including the maintenance ofcell functions, differentiation, and the response to stress, is tightlyregulated by autophagy, which is a cell survival mechanism foreliminating and recycling damaged proteins and organelles. With theimportant roles in the maintenance of cellular homeostasis and organfunction, autophagy has emerged as a potential target for the preventionand treatment of osteoporosis. Apart from supplementation with calciumand vitamin D, the treatment for osteoporosis includes a variety ofdrugs with different mechanisms of actions; such drugs includebisphosphonates, selective estrogen receptor modulators, teriparatide,and denosumab. Adverse events may occur during treatment, however,including mandibular osteonecrosis, nephrotoxicity, and increased tumorrisk. Therefore, novel therapeutic targets to reverseosteoporosis-related bone loss and to otherwise treat and preventosteoporosis are urgently required.

As a progressive disease without any effective curative treatment, thereis a long felt but unsolved need to find a treatment for, to prevent andto reduce the likelihood of osteoporosis so as to improve the quality oflife for the many existing and future individuals who would otherwisesuffer from this tragic disease.

With the aging population, the frequency of osteoporosis is increasing,which usually decreases bone strength, mass, and density and increasesfragility, often leading to fractures. The misconception is thatosteoporosis is a “women’s disease.” While the disease is more common inwomen, men are also at risk for osteoporosis. As many as 2 millionAmerican men already have osteoporosis, the bone thinning that makesbones brittle and porous and at likely to fracture. Osteoporosis affectsabout one in five women over age 50, but only one in 20 men. Amongwomen, those of White and Asian descent are more likely to developosteoporosis.

Osteoporosis is the most prevalent metabolic bone disease, characterizedby low bone mass and microarchitectural deterioration of bone tissue.According the International Osteoporosis Foundation, more than 200million people worldwide suffer from osteoporosis and there is anaverage fracture caused by osteoporosis every 3 years, and the incidenceof hip fracture has been increasing in the world since 1990, which isexpected to increase by 240% in women and 310% in men by 2050.

Osteoporosis is one of the most frequent skeletal disorders and a majorcause of morbidity and mortality in the expanding aging population.Current approaches to treat osteoporosis work primarily throughinhibiting bone absorption and promoting bone formation, but the sideeffects of anti-osteoporosis drugs pose a huge challenge in practice,and thus, there is a long felt but unsolved need to provide newtreatment strategies for osteoporosis.

SUMMARY OF THE INVENTION

The gut microbiota reportedly plays a key role in bone development.Aspects of the present invention are directed to the modification ofperson’s microbiome, and particularly one’s gut microbiome, to reducethe risk of osteoporosis. The gut microbiome impacts metabolichomeostasis mainly by secretion of metabolites and modulation of thehost immune systems. Short chain fatty acids (SCFAs) secreted by the gutmicrobiome induces an increase in the transcription of calcium bindingproteins in human and murine Caco-2 cells. Butyric acid regulatesintestinal regulatory T cell proliferation and enhances osteoclastdifferentiation. In addition, the gut microbiome also maintains bonehomeostasis by regulating calcium absorption-related proteins andmodulating tight junction proteins.

One aspect of the present invention relates to a method for treating orpreventing a bone disease or increasing bone strength in a mammaliansubject comprising administering a pharmaceutical formulation thatincludes tomatidine, rapamycin and/or xylitol, alone or together with aprobiotic composition administered to the gastrointestinal system of theindividual. Preferably the probiotic bacteria include one or more of thefollowing: Lactobacillus reuteri, Lactobacillus acidophilus,Lactobacillus rhamnosus, Akkermansia muciniphila, Bifidobacteriaceae, F.prausnitzii, Roseburia, Veillonella, and Coprococcus. Another aspect ofthe present invention is to reduce the numbers of certain bacteria in anindividual to avoid osteoporosis, with such bacteria selected from thegroup consisting of Actinomyces, Eggerthella, Clostridium Cluster XIVa.

The gut microbiome is known to modulate immune cell activities.Alterations in the microbiome have previously been associated withinflammatory conditions. Osteoporosis occurrence is accelerated inpatients with immune-mediated inflammatory conditions, where excessiveproduction of pro-inflammatory cytokines leads to increased osteoclasticbone resorption. Thus, modifying an individual’s gut microbiome toaddress inflammatory conditions is one route to reducing the likelihoodof osteoporosis. In certain embodiments, bacteria able to generatebutyrate are employed to reduce the likelihood of osteoporosis, asbutyrate, as well as other short chain fatty acids, is known tostimulate bone formation. For example, in certain embodiments, thelevels of F. prausnitzii, Veillonella, and/or Coprococcus are increasedin an individual to treat, prevent or reduce the likelihood ofosteoporosis.

One aspect of the present invention is directed to the inclusion ofxylitol in various formulations and the administration thereof toindividuals so as to prevent the likelihood of osteoporosis, as well asto prevent and treat the disease. Xylitol is a pentitol used as asweetener and as a platform chemical for the production of industriallyimportant chemicals. Xylitol has good gastrointestinal tolerance andtherefore is considered safe and effective when consumed by humans. Asfurther described below, various formulations include xylitol togetherwith tomatidine and/or rapamycin to treat, prevent and reduce thelikelihood of osteoporosis.

As described in more detail herein, one aspect of the present inventioninvolves the use of a natural small molecule derived from tomato plants,tomatidine, to prevent and/or treat osteoporosis. Tomatidine is believedto cause cell growth, especially in skeletal muscle tissue. Tomatidineis the aglycone derivative of tomatine, an abundant glycoalkaloid intomato plants that mediates plant defense against fungi, bacteria,viruses and predatory insects. When consumed by animals, alpha-tomatineis hydrolyzed by stomach acid and intestinal bacteria to tomatidine,which is absorbed by the gut. Tomatidine has a variety of biologicalactivities and as described herein, is an effective agent informulations designed to combat osteoporosis and related muscle wastingdiseases.

Tomatidine is an inhibitor of muscle atrophy and thus has a use as atherapeutic agent for skeletal muscle atrophy. Tomatidine is believed tohave an anti-atrophic (anabolic) effect in skeletal muscle and possessesanti-hyperlipidemic and anti-atherosclerotic effects without evidence oftoxicity. Tomatidine is significantly more potent than ursolic acid inbuilding muscle tissue and has a different mechanism of action.Tomatidine is associated with anti-apoptotic, anti-inflammatory,anti-bacterial, and anticancer properties. Tomatidine suppressesinflammation in LPS-stimulated murine macrophages by inhibiting theNF-_(k)B and JNK signaling pathways.

The tomato belongs to the Solanaceae family that includes more than3,000 species. Tomato fruit consumption has been associated with areduced risk of inflammatory processes, cancer, and chronicnoncommunicable diseases (CNCD) including cardiovascular diseases (CVD)such as coronary heart disease, hypertension, diabetes, and obesity.Tomatidine is found in certain plants at certain developmental stages,such as in green (but not ripened red) tomatoes. One aspect of thepresent invention is directed to the provision to individuals in needthereof with effective amounts of tomatidine to address osteoporosis.

In various embodiments of the present invention, tomatidine, alone or incombination with other agents, e.g. xylitol and/or rapamycin, isemployed to reduce the likelihood of an individual experiencingosteoporosis and to otherwise treat and to also prevent the disease.

Rapamycin was first discovered in Easter Island soil bacteria in the1980s. It is known that rapamycin extends the life span of mice. Theprotein that rapamycin targets is a kinase called mTOR. This kinaseplays a role in a variety of pathways. Rapamycin is an inhibitor of mTORcomplex (mammalian target of rapamycin) which is a serine threoninekinase and a master regulator of protein synthesis, cell growth, andcell metabolism. Excessive mTORC1 activity has been implicated inmultiple disease conditions, as well as various cancers, inflammatorybowel disease, inflammatory skin diseases and neurodegenerativediseases. In various embodiments of the present invention, rapamycin isemployed, especially in combination with other agents, e.g. tomatidineand xylitol, to treat, prevent and to reduce the likelihood of anindividual suffering from osteoporosis.

Sirolimus (rapamycin) has to date two approved indications--renaltransplantation and lymphangioleiomyomatosis and has also been shown tobe potentially effective in treating Tuberous Sclerosis Complex(TSC)-associated seizures, skin disease, brain lesions, pulmonarylesions, and renal lesions. In various embodiments as described herein,administration of therapeutically effective amounts of rapamycin,directly by either aerosol administration, injection, oraladministration, rectal administration, or via an individual’smicrobiome, forms one aspect of various embodiments of the presentinvention. Such employment of an anti-aging medicine like rapamycin isbelieved to be one of the most effective ways to combat variousage-associated diseases of aging people, including osteoporosis.

In certain embodiments, DNA encoding pre-cursors for the biosynthesis oftomatidine, xylitol and/or rapamycin and its analogs is inserted intothe genome of one or more bacterial species by employing CRISPR-Cas orCPf1 systems, such that an individual can orally take a pill containingsuch modified bacteria (preferably bacteria of the same species aspresently reside in the individual’s gut microbiome) and in such amanner, effectively administer tomatidine, xylitol and/or rapamycin tothe individual in a manner that does not require injections or thetaking of traditional pharmaceutical formulations. In such a manner, theproduction by such bacteria inside the individual provides a morenatural way for to address the ravages of osteoporosis. Administeringone or more of tomatidine, xylitol and/or rapamycin, especially inconcert with the modification of an individual’s gut microbiome asdescribed herein, is able to maintain and/or restore the health of anindividual, especially those subject to osteoporosis.

In certain embodiments, and while not bound by theory, it is believedthat tomatidine increases the ability of an individual to not onlymaintain muscle mass, but to treat osteoporosis, while rapamycin, as aninhibitor of mTOR, addresses still further aspects of the disease, asdoes xylitol. The combination of these three ingredients in aformulation is one of a variety of preferred embodiments as disclosedherein. It is believed that these three agents may play parallel butseparate roles in muscle atrophy, and thus, the use of these agents toaddress osteoporosis is one particular aspect of the present invention.

By administering tomatidine to an individual to maintain desired musclemass, while also co-administering rapamycin to such individual toinhibit the growth of certain cells, especially cancer cells, one isable to achieve the seemingly converse objectives of maintaining musclemass so as to preserve the health of an individual, while simultaneouslydefeating the undesired growth of cancer cells by the administration ofeffective amount of rapamycin to inhibit such undesired growth. Xylitolassists in halting the progression of osteoporosis, with its mechanismof action not fully understood.

The administration of such compounds/agents via an individual’smicrobiome is one potential way to avoid the disadvantages of othermodes of administration. The administration of the describedformulations of the present invention have the positive effect ofextending the lifespan of an individual, and especially effective indelaying the onset of age-related diseases and conditions, such ascancer and osteoporosis, thus extending the healthspan of the individualfrom what it otherwise would have been if such administration was notperformed. The particular effective amount of such agents/compounds,such as rapamycin, tomatidine and xylitol (including analogs orderivatives thereof) depend upon the stage of the disease, the length ofduration of treatment desired and the particular characteristics of theindividual’s health and microbiome characteristics. One of skill in theart will understand, given the guidance provided herein, the particularaspects of administration of such formulations. In certain embodimentswhere the agent/compound comprises rapamycin or an analog thereof,administration of rapamycin may be performed to affect about 0.001 mg to30 mg total per day as an effective dose, preferably at least about 0.1mg per day, with a preferred blood level of rapamycin in the subjectbeing about 0.5 ng per mL whole blood after administration of thecomposition after a 24 hour period. In embodiments where genes thatencode one or more precursors for the biosynthesis of rapamycin,tomatidine and xylitol, by administering antibiotics that target theparticular microbes that produce such agents/compounds/ precursors, onecan address overproduction by such microbes by killing the microbesproducing such agents. One of ordinary skill in the art will appreciatefrom written materials predating this application the appropriate dosesand modes of administration of any one of these three agents.

In particular embodiments, the present invention is specificallydirected to a method of treating osteoporosis in a subject in need ofsuch treatment by administering a therapeutically effective amount of acomposition comprising tomatidine, either alone or in conjunction withxylitol and/or rapamycin. Other embodiments further includeadministering to an individual suffering from osteoporosis atherapeutically effective amount of one of xylitol, tomatidine and/orrapamycin separately, rather in a combined formulation, with the modesof administration of each of these potentially being different, e.g. oneorally, one inhaled, etc.

It will be appreciated that still other aspects of the present inventioninvolve the treatment of obesity (as well as various forms of cancer) byproviding certain amounts of tomatidine via a person’s microbiome tofacilitate muscle mass increases, while at the same time, decreasing theamount of fat weight of the individual being administered thetomatidine.

Other aspects of the present invention relate to the reduction of thelikelihood of, treatment and/or prevention of osteoporosis byinterrupting a microbial pathway, and by addressing muscle atrophyassociated with osteoporosis. Osteoporosis is usually managed with aclass of popular drugs—bisphosphonates—that reduce bone resorption. Twoof the most common orthopedic disorders are osteoporosis andosteoarthritis. In certain embodiments of the present invention,bisphosphonates are included in formulations that otherwise includetomatidine, as well as xylitol and/or rapamycin.

Various embodiments of the present invention use microbiotamodifications to improve the efficacy of existing treatments, and inparticular, the provision of tomatidine, alone or in conjunction withmodifications to a patient’s microbiome, e.g. by increasing the presenceof microbes that produce SCFA, and especially butyrate, is one aspect ofthe present invention. Other embodiments further employ the modificationof an individual’s microbiome, alone or in combination with theadministration of formulations that include one of tomatidine, rapamycinand/or xylitol, to treat and prevent the progression of osteoporosis.One aspect of the present invention involves the maintenance of thelevel of Prevotella in an individual as such bacterium is closelyrelated to the occurrence of inflammatory bone loss. Prevotellafunctions through microbe associated molecular patterns (MAMPs) toactivate various toll-like receptors (TLRs) and through principal immunecells to release inflammatory mediators and promote chronicinflammation. Thus, in various embodiments, the reduction in Prevotellacan reduce the likelihood of osteoporosis. Antibiotics or the selectivereduction of Prevotella using CRISPR-systems can be employed to achievethis objective.

Short-chain fatty acid production by commensal bacteria is important inregulating the immune system in the gut. Butyrate plays a direct role ininducing the differentiation of regulatory T cells and suppressingimmune responses associated with inflammation. Butyrate is normallyproduced by microbial fermentation of dietary fiber and plays a centralrole in maintaining colonic epithelial cell homeostasis and barrierfunction. Various embodiments described herein promote the production ofbutyrate via increased numbers of beneficial bacteria (e.g. Coprococcus,Roseburia, Bifidobacterium, and Faecalibacterium prausnitzii) and/or theuse of modified microbes (e.g. via the employment of CRISPR-systems)administered to an individual, alone or in concert with the variousother agents as described herein to effectively treat or prevent or toreduce the likelihood of osteoporosis.

Preferably, the bacteria employed in certain embodiments of the presentinvention are administered orally to a patient. In certain embodiments,CRISPR engineered bacteria are used that are non-pathogenic and may beintroduced into the gut in order to reduce gut inflammation and/orenhance gut barrier function. For example, in some embodiments, thebacteria are under the control of a RNS-responsive regulatory region anda corresponding RNS-sensing transcription factor such that a desiredproduct, e.g. butyrate, is produced, which induces the differentiationof regulatory T cells in the gut and/or promotes the barrier function ofcolonic epithelial cells.

Still other embodiments are directed to the modification of anindividual’s microbiome to influence various aspects of their metabolismin a manner that not only retains and maintains the ability to nurturemuscle tissue, but to also reduce obesity by affecting the amount of fatthat the body stores, and further, to address the progression ofosteoporosis. While not bound by theory, it is believed that the gutbacteria of an individual is a substantial source of acetate production.The production of acetate by gut microbes is believed to send signals tothe brain of the individual to initiate the production of insulin,conveyed via the vagus nerve. Fine tuning of the amount and type of gutmicrobes (e.g. via the use of antibiotics or CRISPR systems to initiallyreduce the kind and numbers of undesired bacteria, followed bypurposeful inoculation of an individual’s gut microbiome with desiredand/or modified microbes, e.g. via CRISPR-Cas insertion of particularfactors, proteins, etc., such as precursors for tomatidine, xylitol orrapamycin), the administration of tomatidine and/or xylitol and/orrapamycin, etc. is an effective way to address not only muscle wastingand osteoporosis issues, but also obesity issues of individuals.

One embodiment of the present invention is directed to a bioadhesivestrip adapted to bind to a mucosal membrane for at least 1 hour whileinside a person’s mouth, where the strip includes tomatidine and xylitolin an amount sufficient to reduce the likelihood of osteoporosis. E.g.at least 10 micro-mole of tomatidine and at least 200 mg of xylitol orat least 0.2% xylitol by weight. In preferred embodiments, the stripincludes at least one polymer selected from the group consisting ofpullulan, hydroxypropylmethyl cellulose, hydroxyethyl cellulose, sodiumalginate, polyethylene glycol, tragacanth gum, guar gum, acacia gum,arabic gum, carboxyvinyl polymer, amylose, high amylose starch,hydroxypropylated high amylose starch, dextrin, chitin, chitosan, levan,elsinan, collagen, zein, gluten, soy protein isolate, whey proteinisolate, casein and mixtures thereof.

Certain embodiments of the present invention are directed to a methodfor reducing the likelihood of osteoporosis in an individual human beingby substantially reducing a human being’s resident population of gutmicrobes prior to administering a therapeutically effective amount of abacterial formulation comprising Coprococcus. Provision of fructan fiberinulin is preferably done in an amount sufficient to reduce the pH inthe colon of the human being to achieve acidifying of the colon, whichalso supports the maintenance of the Coprococcus bacteria. In preferredembodiments, the beneficial formulation is encapsulated. Suchencapsulation is done to preserve the viability of various bacteria thatwould otherwise be adversely affected by stomach acids and/or aerobicenvironments. See, e.g. U.S. Pat. No. 10576113 Madhavamenon, et. al,incorporated herein by this reference. In still other embodiments, theCoprococcus bacteria employed are first isolated from a human being’sstool and are from the human being treated. One important aspect ofcertain embodiments of the present invention involves the administrationof tomatidine to the human being to combat osteoporosis, withformulations thereof similarly encapsulated to preserve potency andefficacy. In still other embodiments, the method for reducing thelikelihood of osteoporosis involves the use of bacteria modified via aclustered regularly interspaced short palindromic repeats (CRISPR)CRISPR associated protein (Cas) system or a CRISPR from Prevotella andFrancisella 1(Cpf1) system. For example, CRISPR systems can be used toselectively reduce the numbers of certain bacteria often foundassociated with osteoporosis, such as Actinomyces, Eggerthella, andClostridium Cluster XlVa. In other embodiments, there is a reduction ofbacteria in the gut of the human being, wherein the bacteria reduced areselected from the group consisting of Pediococcus, Streptococcus,Enterococcus, and Leuconostoc bacteria.

In particular embodiments, the step of reducing the number of bacteriacomprises administering an antibiotic. Moreover, reducing the number ofbacteria in the human being’s gut using a clustered regularlyinterspaced short palindromic repeats (CRISPR) CRISPR associated protein(Cas) system or a CRISPR from Prevotella and Francisella 1 (Cpf1) systemis effective and has advantages over the use of a general antibiotic. Inpreferred embodiments, inclusion of a bacterium selected from the groupconsisting of Chlamydia, Shigella flexneri, Mycoplasma bacteria,Lactobacillus casei, Roseburia, Bifidobacterium, and Faecalibacteriumprausnitzii is accomplished to reduce the likelihood of osteoporosis.Another aspect of the present invention is directed to increasing thelevels of bacterial genera selected from the group consisting ofBifidobacterium, Lachnospira, Roseburia, Lactobacillus and Shigella.

In still further embodiments, a population of beneficial bacteriaselected from the group consisting of Coprococcus, Roseburia,Bifidobacterium, and Faecalibacterium prausnitzii, is administered, aswell as fiber to the individual to maintain a therapeutically effectiveamount of the beneficial bacteria in the gut of the individual. Theindividual is then administered at least 10 micro-mole of tomatidine.

In other embodiments, the gut of the individual is provided with aLactobacillus species and at least 6 grams per day of fiber to maintaina therapeutically effective amount of the beneficial bacteria in the gutof the individual human being. Preferably, in still other embodiments,the levels of at least one of Roseburia and Faecalibacterium prausnitziiare increased in the individual’s gut microbiome. In some embodimentsthe step of reducing the number of bacteria in the human being isachieved using an antibiotic or using a clustered regularly interspacedshort palindromic repeats (CRISPR) CRISPR associated protein (Cas)system or a CRISPR from Prevotella and Francisella 1 (Cpf1) system toselectively kill or reduce the number of undesired bacteria. In otherembodiments the levels of bacteria are increased, such bacteria selectedfrom the group consisting of Bifidobacterium, Prevotella, Lachnospira,and Shigella, alone or together with the administration of at least oneof xylitol, tomatidine and rapamycin. Certain embodiments of theinvention are directed to providing in the gut of an individual apopulation of beneficial bacteria selected from the group consisting ofFaecalibacterium prausnitzii and/or Akkermansia muciniphila;administering at least 6 grams per day of fiber to the individual tomaintain a therapeutically effective amount of the beneficial bacteriain the gut of the individual human being; and administering tomatidine(in an effective amount) to the individual human being. In still otherembodiments, the present invention includes administering to theindividual human being a bacteria selected from the group consisting ofStreptococcus, Actinomyces, Veillonella, Fusobacterium, Porphyromonas,Prevotella, Treponema, Neisseria Haemophilus, Lactobacillus,Capnocytophaga, Eikenella, Leptotrichia, Peptostreptococcus,Propionibacterium, Chlamydia, Shigella flexneri, Mycoplasma bacteria, H.pylori, and Streptomyces hygroscopicus. To reduce the likelihood ofosteoporosis, various embodiments include administering to an individualan effective amount of a formulation comprising at least two of: atleast 10 micro-mole tomatidine, at least 0.1 mg of rapamycin and atleast 200 mg of xylitol. Particular embodiments employ an oral strip todeliver the agents as described herein. For example, one embodimentinvolves the administration of one of tomatidine, xylitol and rapamycinto individuals by using a bioadhesive strip having a first and secondside, the second side having a bioadhesive that is adapted to bind to amucosal membrane for at least 1 hour while inside a person’s mouth. Suchstrip includes at least one polymer selected from the group consistingof pullulan, hydroxypropylmethyl cellulose, hydroxyethyl cellulose,sodium alginate, polyethylene glycol, tragacanth gum, guar gum, acaciagum, arabic gum, carboxyvinyl polymer, amylose, high amylose starch,hydroxypropylated high amylose starch, dextrin, chitin, chitosan, levan,elsinan, collagen, zein, gluten, soy protein isolate, whey proteinisolate, casein and mixtures thereof; wherein said strip includes one oftomatidine or xylitol.

The gut, vaginal, and urinary microbiomes are mutually influential, anddysbiosis of one of these microbiota results in several health problems.Menopause alters the gut, vaginal, and urinary microbiota due to drastichormone changes. The gut microbiome of women influences bone metabolismand has a profound effect on bone quantity, quality, and overallstrength. The gastrointestinal tract contains the highest concentrationof immune cells that communicate with the microbial community, whichtriggers a release of metabolites that affect the immune systemdirectly. The intestinal epithelial barrier plays a crucial role inseparating the internal structures, with intestinal epithelial cellsbeing sealed by tight junction proteins, such as ZO-1, claudin-1, andoccludin. One aspect of various embodiments of the present invention isdirected to altering the expression of tight junction proteins to alterthe permeability of the intestinal barrier. lf the intestinal barrier isbreached, it allows microorganisms to enter the subepithelial structuresfrom the intestinal metastatic lumen, and triggers an inflammatoryresponse, often resulting in the development of osteoporosis, especiallyin postmenopausal women. Various embodiments of the present inventionare directed to increasing probiotic function to increase the strengthof the intestinal epithelium by upregulating tight junction proteins,reducing antigen presentation and activation of intestinal immune cells,which leads to changes in the bone mineral density.

In various embodiments, Lactobacillus rhamnosus is employed as it isbelieved to be advantageous in promoting osteogenesis, which may beresponsible for the alleviation of osteoporosis. In various embodiments,and while not being bound by theory, the provisioin of L. rhamnosus isbelieved to alleviate osteoporosis by modulating the gut microbiome andintestinal barrier and improving Th17/Treg balance in gut- bone.

Reduction of Lactobacillus is closely associated with osteoporosis.Thus, aspects of the present invention are directed to increasing thepopulation of Lactobacillus in the guts of individuals who arecandidates for suffering from osteoporosis. Estrogen deficiency isbelieved to impair the intestinal barrier, and leads to increasedintestinal permeability, resulting in increased expression ofpro-inflammatory factors in the intestine and bone, which disrupts bonemetabolism. The provision of L. rhamnosus to adjust the gut microbiomestructure and metabolism, improves the inflammatory status, and acts toameliorate osteoporosis. The provision of L. rhamnosus is intended tomodulate the gut microbiota by increasing the abundance of Bacteroidetesand the levels of the butyrate-producing genes, such as But and Buk, topromote butyrate production. Various embodiments are focused on theinterventional targets of gut barrier function and the production ofSCFAs to trigger gut-bone signaling pathways that implement thetreatment of osteoporosis and other bone diseases.

In various embodiments of the present invention, bacteria areadministered to women to reduce the pH of their vaginas where thereduction of estrogen production has resulted in an increase of vaginalpH. This is accomplished by the administration of bacteria that affectthe vaginal pH, notably the administration of Lactobacillus so as topositively influence the changes that are otherwise observed in vaginalstructure and function in view of the onset of genitourinary syndrome ofmenopause. Menopause alters the gut microbiota, which has severaleffects on a woman’s health. The urinary microbiome plays an importantrole in urinary tract disease In the ovulatory cycle. Certain hormoneshave substantial effects on the composition of the microbiome. Estrogenand progesterone cause thickening of the stratified squamous epitheliumof the vagina, deposition of glycogen, and local immunity. Alterationsin the microbiota due to postmenopausal hormone changes are similar tovaginal dysbiosis observed in inflammatory pelvic disease, humanimmunodeficiency virus and human papillomavirus (HPV) infections, andpregnancy. Urinary pathogens are believed to originate in thegastrointestinal tract, with an intermediary step of vaginalcolonization. Therefore, changes in the gut and vaginal microbiome as aresult of dramatic hormonal changes during menopause impact the urinarymicrobiome. One aspect of many embodiments of the present invention isdirected to modulation of the changes in a woman’s microbiome due topostmenopausal changes to alleviate and control postmenopausal health.Menopause-induced hormonal changes significantly alter the gutmicrobiome and hormone therapy can restore the microbiome to somedegree. Postmenopausal women have a higher Firmicutes/Bacteroidetesratio and a higher relative abundance of Lachnospira and Roseburiacompared to premenopausal women, while premenopausal women have a lowerrelative abundance of the Prevotella, Parabacteroides, and Bilophilagenera. Increased Bilophila in menopausal women leads to increasedhydrogen sulfide production, inducing local inflammation and mucosaldamage, increased serum endotoxin concentrations, and inflammatoryreactions in several types of tissues. Thus, various embodiments of thepresent invention are directed to modulation of an individual’smicrobiome to affect such changes by effective administrations ofparticular bacteria.

Various embodiments are directed to balancing a woman’s microbiome byincreasing populations of gut microbiome imbalance due to a deficiencyof Aggregatibacter segnis, Bifidobacterium animalis, and Acinetobacterguillouiae. Moreover, other embodiments are directed to increasingpopulations of

Romboutsia, Mollicutes, and Weissella spp. and in reducing populationsof Fusicatenibacter, Lachnoclostridium, and Megamonas spp.

Certain embodiments of the present invention are directed to themodulation of an individual’s gut microbiome so as to regulate bone massby altering immune status, intestinal calcium absorption, and affectingosteoclasts-mediated bone resorption. Such modulation of the gutmicrobiome is to maintain bone mass and bone quality in an individual.

The gut microbiome exerts effects in an individual’s skeletal system asit modulates gut permeability, hormonal secretion, and immune response,and stimulates calcium and vitamin D absorption. The gut microbiomeregulates bone remodeling, which is mediated by osteoclasts with respectto bone resorption functions and with osteoblasts with respect to boneformation. The gut microbiome further plays a role in the ability ofbones to respond to mechanical load and bone strength.

In contrast to current anti-osteoporosis drugs, such as thebisphosphonate, calcitonin, cathepsin K inhibitors, and estrogen, thatare believed to reduce bone heterogeneity and thereby enhance the riskof bone fragility and fractures, embodiments of the present inventionrely upon the modulation of an individual’s gut microbiome to achievemore healthful results, including the reduction in the decrease of bonemass, bone microstructure destruction, and decreased angiogenesis. Forexample, in certain embodiments, Lactobacillus strains, preferably acombination of at least two of Lactobacillus paracasei and Lactobacillusplantarum at a dose of 1 × 10¹⁰ CFU per day, is believed to reduce boneloss in an individual, as compared with a person who was notadministered such Lactobacillus strains. Thus, various embodiments ofthe present invention are directed to the modification of anindividual’s gut microbome via the ingestion of probiotics as a viabletherapeutic strategy to regulate bone metabolism to address bone lossand osteoporosis. The modulation of the gut microbiome in certainembodiments involves improving the proportion of Firmicutes vs.Bacteroidetes, inducing the proliferation of beneficial microbiota in anindividual’s gut, and improving the function of intestinal mucosalbarrier, which all thereby further positively modulate the bonemetabolism.

Many drugs for the treatment of osteoporosis have severe side effectsand are not suitable for long-term use. The present invention providesan effective and a safer treatment strategy than conventional drugs,focusing on gut microbiome disorders as an important pathogenic factorin osteoporosis. Thus, embodiments of the present invention provide agut microbiome targeted treatment for osteoporosis that involves theadministration of probiotics to address this disease.

Oral probiotics have limitations: the constant updating of intestinalmucus in the gastrointestinal tract makes it difficult for probiotics tocolonize; there is a limited time of residency in an individual’s gutand thus, repeated doses of probiotics is required; and acidic gastricjuices can inactivate probiotics. Use of nano-level protective shellsare preferably used to protect the probiotics from stomach acids.Polyethylene glycol or its derivatives, is preferably employed toenhance mucus penetration of microbes. Thiopolymers are also preferablyused as a bridge connecting probiotics and mucus to achieve long-termadhesion of the probiotics to mucus membranes. Hydrogel microsphereswith probiotics-loads can be used for effective administration ofdesired bacteria. Indeed, a synergistic prebiotic/postbiotic deliveryvia micro-capsules is preferably employed to significantly increase theoverall abundance and richness of beneficial bacteria, particularlybacteria that produce SCFAs, and particularly those bacteria thatproduce butyrate. Combining probiotics and prebiotics in oneencapsulation (whether it be sub-divided within an outer capsule) is oneway to introduce to the lower gut desired microbiota-modulatingmaterial, including both beneficial bacteria and functionally richingredients, thus treating osteoporosis. In certain embodiments,chitosan and its derivatives are used to reversibly open tight junctionsbetween adjacent intestinal cells due to their positively chargedproperties. Probiotics are selected that promote bone formation andadministered, preferably orally, so as to treat osteoporosis.

Certain embodiments of the present invention include the use ofHesperidin (hesperetin-7-O-rutinoside), a flavanone glycoside highlyabundant in citrus fruits, particularly in oranges. In variousembodiments, tomatidine is employed as a treatment of osteoclast-relateddisorders, including osteoporosis. Tomatidine is a natural steroidalalkaloid that isolated from the Solanaceae plants such as tomatoes,potatoes and eggplants and is known to be a nitrogen analogue of steroidsaponins and a precursor of steroidal hormones and anti-inflammatorysteroids. Tomatidine suppresses osteoclast formation and mitigatesestrogen deficiency-induced bone mass loss, and is effective to treatrheumatoid arthritis.

Resveratrol (3,5,4′-trihydroxy-trans-stilbene) is a natural polyphenoliccompound found in several plants, including grapes, berries, andpeanuts. Resveratrol, a natural polyphenolic compound, is employed as atreatment of osteoporosis and other bone diseases due to its impact onthe MDM2/p53 signaling pathway. MDM2-mediated p53 degradation inducesosteoblast differentiation, and resveratrol is believed to partiallyreverse p53-dependent inhibition of osteogenic differentiation. Thus,resveratrol is employed in various employments to alleviate osteoporosisby modulating the MDM2/p53 signaling pathway. The p53 signaling pathwayhas been identified as a key Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway involved in the protective effects of resveratrol onosteoporosis. Resveratrol can counteract the negative effects of p53 onMDM2-mediated osteogenic differentiation. MDM2 induces p53 degradationand promotes osteogenesis.

MDM2-mediated inhibition of p53 induces osteoblast differentiation. p53is enriched in osteoporosis. Resveratrol-targeted genes exert biologicaleffects primarily through the p53 signaling pathway. p53 inhibits cancerdevelopment and progression via several mechanisms, including apoptosis,regulation of DNA replication, cell division, and inhibition ofangiogenesis. The p53 protein is encoded by the TP53 gene.

Certain embodiments are directed to modulating an individual’smicrobiome as described herein, in addition to the administration ofparticular drugs, such as the humanized monoclonal antibodies, such asromosozumab, able to bind to sclerostin and thereby prevent itsinhibitory effect and activate the Wnt signaling pathway, leading tobone formation and bone mineral density gain, promoting osteogenesis andinhibiting bone resorption, and increasing cortical and trabecular bonemass.

In addition to osteoporosis, the present invention in variousembodiments is also directed to treating or avoiding chronic fatiguesyndrome, as an individual’s gut microbiome plays an important role insuch syndrome, which some have associated with long COVID. As a chronicbone disease, osteoporosis mainly includes diabetes induced osteoporosisand postmenopausal osteoporosis. Diabetes induced osteoporosis is due toinsulin deficiency and endocrine dysfunction leading to bone densitydecline and bone microstructure changes, while postmenopausalosteoporosis is bone loss caused by estrogen deficiency. The commonpathogenesis of the two types of osteoporosis is that bone formationmediated by osteoblasts is less than bone resorption mediated byosteoclasts, resulting in an imbalance in bone homeostasis. One aspectof various embodiments involve mitochondrial function, which isessential to improve bone homeostasis. Mitochondrial quality control isof great significance for homeostasis of the mitochondrial network andnormal mitochondrial function. The accumulation of damaged mitochondriais generally prevented by mitophagy, a type of organelle-specificmacroautophagy that is impaired in some tissues in aging and age-relateddiseases. Interventions that promote mitophagy, such as administrationof tomatidine are employed in various embodiments to extend healthspans.

The mitochondrial functions of targets in the pathophysiology ofosteoporosis are various. Certain embodiments include the use offerroptosis, which is a key mechanism regulating bone formation andresorption, and mitochondrial function can regulate ferroptosis. Someembodiments are directed to mitochondria-related mechanisms and noveldrug targets for the prevention and treatment of osteoporosis.Ferroptosis is a form of programmed cell death caused by iron-dependentlipid peroxidation and plays a key role in the pathological progressionof MAFLD/NAFLD. Indeed in certain embodiments, and inhibition offerroptosis is employed as a therapeutic strategy for the treatment ofNAFLD. Gut microbiota dysbiosis usually reduces beneficial bacteria andchanges small intestine mucosal barriers, increasing intestinalpermeability and microbial metabolites such as LPS and short chain fattyacids. In certain embodiments, a probiotic comprised of Lactobacillus,Bifidobacterium, Streptococcus is used to assist in the recovery ofliver enzymes in patients with NAFLD. As NAFLD is closely related toobesity, eating foods rich in fat and fructose alters the intestinalmicrobiota, changes intestinal barrier function, and causes endotoxemiaand inflammatory reactions, all of which promote obesity and NAFLD.Thus, in certain embodiments, those with NAFLD should reduce theirweight so as to reduce liver fat deposition and inflammatory responses.

Iron overload is prevalent in NAFLD patients, and iron imbalance isassociated with obesity. It is noted that NAFLD and alcoholic fattyliver disease are pathologically similar and are believed to have commonpathogenic mechanisms, such as the increased expression ofalcohol-metabolizing enzymes (i.e. ADH) in patients with NASH. Increasedacetaldehyde levels further increase small intestine mucosa permeabilityand with the increase in absorption of intestinal microbiotametabolites, NASH is promoted. Decreased abundance of A. muciniphila isrelated to thinning of the mucus layer and increased inflammation, whichpromotes alcoholic and nonalcoholic liver damage. When intestinalpermeability increases, microorganisms and microorganism-derivedmolecules are transferred to the liver through the gut-liver axiscausing inflammation and liver damage. As acetic acid, propionic acid,and butyric acid are involved in the expression of fatmetabolism-related genes, such SCFAs protect the liver by reducingintestinal mucosa permeability through the gut-liver axis and inhibitingendotoxin translocation.

Certain embodiments of the present invention are directed to the use ofbutyric acid, preferably bacterially generated, to regulatemitochondrial function, as a therapeutic strategy to combat obesity.

P. gingivalis affects the intestinal microbiota composition such that itwas biased towards the increased production of some amino acids andinflammatory factors, which are then absorbed into the liver, activatinghepatocyte ferroptosis, and causing NAFLD. P. gingivalis generates anabnormal hepatic inflammatory response and abnormal function ofglutamate, glutamine and other components of amino acid synthesis aftercolonization in the liver. NAFLD is recognized as the most frequentlydiagnosed form of liver disease around the world, but the causes andmechanisms underlying its progression are not completely understood. TheCertain embodiments of the present invention are directed to themodulation of gut microbiota as a mechanism that affects thepathogenesis of NAFLD. The reduction of P. gingivalis is one focus assuch bacteria has been found to accelerate the development of NAFLD dueto a disordered gut microbiota.

One objective of many embodiments is to modulate the proportions ofBacteroides and Firmicutes in a person as bacteroides have beenidentified as being highly coated with IgA in the intestinal microbiota,which promotes inflammation and drives disease. Chronic systemicinflammatory disease is also associated with reductions in tightjunction protein expression and posttranscriptional modifications.

In various embodiments, nano-level protective shells are preferably usedto protect the probiotics from stomach acids. Polyethylene glycol or itsderivatives, is preferably employed to enhance mucus penetration ofmicrobes. Thiopolymers are also preferably used as a bridge connectingprobiotics and mucus to achieve long-term adhesion of the probiotics tomucus membranes. Hydrogel microspheres with probiotics-loads can be usedfor effective administration of desired bacteria. Indeed, a synergisticprebiotic/postbiotic delivery via micro-capsules is preferably employedto significantly increase the overall abundance and richness ofbeneficial bacteria, particularly bacteria that produce SCFAs, andparticularly those bacteria that produce butyrate. Combining probioticsand prebiotics in one encapsulation (whether it be sub-divided within anouter capsule) is one way to introduce to the lower gut desiredmicrobiota-modulating material, including both beneficial bacteria andfunctionally rich ingredients, thus treating osteoporosis. In certainembodiments, chitosan and its derivatives are used to reversibly opentight junctions between adjacent intestinal cells due to theirpositively charged properties.

As used herein, the treatment of bone disease includes osteoporosis,inflammatory disease, and/or autoimmune diseases, including rheumatoidarthritis. This is because bone tissue consists of extracellularsubstances such as collagen and glycoprotein, and various kinds of cellssuch as osteoblasts, osteoclasts, and osteocytes. The mutual balance ofosteoblasts and osteoclasts is essential for the formation of a healthyskeletal system. Bone metabolism and bone remodeling are important forbalanced activity between the osteoblasts that form a bone matrix andthe osteoclasts that resorb the bone to maintain the homeostasis of thebone. Hormones such as parathyroid hormone (PTH), calcitonin, estrogen,various growth factors secreted from the bone tissue such asinsulin-like growth factor I (IGFI), and cytokines such as tumornecrosis factor-α (TNF-α), regulate the activity balance of osteoblastsand osteoclasts in order to maintain homeostasis. When the balance ofthese osteoblasts and osteoclasts is disturbed, diseases such asosteoporosis or arthritis are induced, which may result resulting inexcessive bone destruction caused by the osteoclasts. Certainembodiments of the present invention are directed to the suppression ofsuch osteoclasts as part of an effective method of treating bonediseases.

Certain aspects of the present invention are directed to methods fordetermining particular bacterial species, specifically those ofBifidobacterium, using computational biology to associate consortia withhealth span and longevity, thus permitting the treatment of age relateddiseases, including increased frailty, osteopenia, osteoporosis, andother bone diseases. For example, certain methods employ a temporalmicrobiome characterization of healthy individuals - such as during thefirst and last stages in life - to elucidate Bifidobacterium that aremost likely to colonize the gut and confer health benefit with thehealth and those that are most likely to colonize, stabilize, andpersist to the latest stages in life, thus compounding benefit to thehost across a lifetime. In certain embodiments, analysis ofBifidobacterium in individuals in a first stage of life that includesinfants and children younger than the age of 18 who have not beenexposed to antibiotics, are compared and contrasted with individuals ina second stage of life, that includes adults of at least threecategories;

-   1) being older than 50 years of age, who have never been exposed to    antibiotics, and who have Bifidobacterium at greater than 1% of    their gut microbiome;-   2) centenarians or super-centenarians; and-   3) menopausal woman without osteopenia and are in the highest    quartile of DXA T-score (or other test associated with bone density    or structure, such as CT scan or ultrasonography) or a menopausal    woman of 65 y/o/a or greater and with a T-score of greater than    -1.0, each group requiring a microbiome comprised of at least 1%    Bifidobacterium.

Based on such assessments, prophylactic treatments for high-riskindividuals can be determined and specific bacteria based therapiesprescribed, whether they be amounts of Bifidobacteria strains to promotean increase in butyrate/ butyric acid in an individual’s gut, etc. totreat a condition or disease state. In certain embodiments,Bifidobacterium isolated from one of the above temporal andcharacteristic thresholds is employed to treat one or more of aging andbone diseases, such as osteoporosis, osteopenia, preferably specificallytailored to address aging, health span, and any chronic disease that isamplified by aging.

Certain aspects of the present invention are directed to the mitigationof the decline of Bifidobacterium in the underlying mechanisms of aging.Bifidobacteria are Gram-positive, anaerobic, non-motile,non-spore-forming, polymorphic rods that belong to the familyBifidobacteriaceae, order Bifidobacteriales and phylum Actinobacteria.The genus Bifidobacterium encompasses approximately 80 species,including four species Bifidobacterium animalis, B. longum, B.pseudolongurp, and B. thermacidophilum. In addition to the presence inthe human gut, bifidobacterial species are present in the human vagina.Certain aspects of the present invention are directed to modulation ofan individual’s microbiome, specifically their gut microbiome, toaddress bone diseases and to reduce the likelihood of osteoporosis. Inaddition to improving the bacterial composition of one’s gut microbiome,certain embodiments further address the abundance of opportunisticpathogens, such as Clostridium sensu stricto, Bacteroides, andIntestinibacter, often observed in individual’s suffering fromosteoporosis. In preferred embodiments, bacteria are administered to anindividual, preferably bacteria known as short-chain-fatty-acid (SCFA)producers, including members of the genera Collinsella, Megasphaera,Agathobaculum, Mediterraneibacter, Clostridium XIV, and Dorea, as suchbacteria have been found to be depleted in individuals suffering fromosteoporosis.

Certain embodiments of the present invention are directed to theemployment of the bacteria Odoribacter due to its production ofshort-chain fatty acids (SCFAs). Short-chain fatty acids (SCFA) areproduced by bacteria dwelling in the large intestine. Butyric acidpresent in the lumen of the gastrointestinal tract is indispensable formaintenance of normal homoeostasis of the mucosa cells as it isresponsible for regeneration and repair processes and has an inhibitoryeffect on the development of other pathogens, such as Escherichia coli,Campylobacter, or Salmonella. While the rapid absorption of SCFA make itdifficult to determine concentrations on the mucous membrane surfaceitself, in preferred embodiments of the present invention, theconcentration of SCFA in the intestinal lumen via the production thereofby bacteria is preferably at least about 8 grams per day, and morepreferably at least about 10 grams per day. In other words, preferably,butyrate concentrations in the intestinal lumen range from between 1 and10 grams per day. To achieve such production in an individual’s gut,preferred embodiments of the present invention call for theadministration of fiber in an amount of at least about 6 grams per dayto feed the SCFA bacteria to produce desired amounts of butyrate.

SCFAs increase fatty acid oxidation and energy metabolism, are involvedin the synthesis of serotonin and stabilizing neurons, and increasecirculating insulin-like growth factor-1, which stimulates osteogenesis.In preferred embodiments, however, due to Odoribacter also generatinghydrogen sulfide, modification of such bacteria may be done to reducenormal levels of hydrogen sulfide generation, thus retaining the desiredSCFA production thereof. Use of Odoribacter to increase levels of SCFAsin menopausal women therefore is a way by which to lower the risk ofosteoporosis. In preferred embodiments, Odoribacter is modified todecrease the amount of hydrogen sulfide produced (as compared to awild-type strain) by at least about 20% while retaining at least theproduction levels of SCFA’s by such naturally occurring bacterium. Invarious embodiments, retention of the normal bacteria flora in terms ofspecies of bacteria is preferred, but while maintaining such diversityof bacteria, the particular strains of such species are modified so asto reduce levels of undesired compounds normally generated by suchbacteria, while at the same time maintaining, if not increasing, thelevel of desired products, such as and particularly, SCFAs. In otherembodiments, beneficial bacteria, namely, bifidobacterial, are employedin methods to reduce the likelihood of osteoporosis or other bonediseases.

While not bound by theory, in certain embodiments, one objective is toincrease the populations of the genera Agathobaculum (Agathobaculumbutyriciproducens and Agathobaculum desmolans), Clostridium XIV,Collinsella, Mediterraneibacter, and Dorea, which contain SCFA-producingspecies. It is believed that such bacteria break down carbohydrates toproduce SCFAs like butyrate, acetate, and propionate, primary energysources for gut endothelial cells. SCFAs, particularly butyrate, induceG-protein-coupled receptors, and aid immune responses, induce Treg cellactivation in the colon, reduce the production of inflammatory cytokineslike NF-κB, and alleviate intestinal inflammation.

It is further believed that butyrate increases the expression ofintracellular calcium transporters to drive an increase in intracellularcalcium absorption.

Thus, one significant aspect of many embodiments is to increase theabundance of SCFA-producing bacteria and their metabolites to reduce thelikelihood of osteoporosis and other bone diseases.

It is also believed that mitophagy is closely related to mammaliantarget of rapamycin (mTOR) signaling and is involved in the occurrenceof osteoporosis, and thus, the administration of rapamycin forms oneaspect of certain embodiments of the present invention. Similarly, it isbelieved that resveratrol plays a protective role in bone loss bypromoting mitophagy of osteoblasts and thus, the targeting of mTORsignaling to enhance mitophagy forms the basis of various embodiments ofthe present invention.

In preferred embodiments, probiotic bacteria such as Bifidobacterium andLactobacillus are employed to improve the condition of an individual’sintestinal mucosa, believed to be directly related to the increase ofbutyrate, butyric acid, etc., especially at levels of production thatexceed (preferably by at least 3 times) those typically available viadosages recommended via over-the-counter supplement products, e.g. about300 mg. a day.

In various embodiments, Bifidobacterium species, and in particular,Bifidobacterium longum subsp. longum, Bifidobacterium adolescentis, andBifidobacterium pseudocatenulatum are employed to modify an adultindividual’s gut microbiome, especially as it relates to the consumptionof dietary carbohydrate, as well as the importance of supplementing suchbacteria following antibiotics. Bifidobacterium species encode anextensive set of glycan-hydrolyzing enzymes which are responsible forspecies- or strain-specific carbohydrate-metabolizing abilities. Thegenomes of B. longum, B. adolescentis, and B. pseudocatenulatum encode awide range of glycan-active enzymes. Bifidobacterium species act asprimary degraders of complex dietary, plant-based carbohydrates, whichin turn would facilitate metabolic cross-feeding with secondarydegraders and lead to higher production of particular hosthealth-associated metabolites such as short-chain fatty acids. Theinfant gut microbiota typically harbors a higher abundance andprevalence of Bifidobacterium bifidum, Bifidobacterium breve, andBifidobacterium longum subsp. infantis (B. infantis) when compared withthat of adults. In healthy adults, the prevalence of Bifidobacteriumgenerally exceeds 90% with just a few species present per subject. Inadults, B. adolescentis and B. longum subsp. longum (B. longum) are themost abundant and prevalent species, as well as B. bifidum and B. breve,but in lower amounts. It is believed that there is a better temporalstability of B. longum, B. adolescentis, and B. bifidum strains.

The functional contributions of bifidobacteria to health and well-beingof adults is largely unexplored, and thus, aspects of the presentinvention are directed to the microbiota enrichment with rationallyselected strains of Bifidobacterium more adapted to the adult host. Andespecially the roles played by Bifidobacterium in the gut ecosystemacross various host ages, and specifically with respect toBifidobacterium animalis subsp. Lactis, and Bifidobacteriumadolescentis, with modulation of an individual’s gut microbiome toreflect that such bacteria are present in at least 20% of relativeabundance in an individual’s gut microbiota. Thus, various embodimentsare directed to the purposeful enrichment of the adult gut microbiotawith Bifidobacterium to support short-and long-term human health.

Certain embodiments of the present invention are directed to methods andcompositions for the maintenance or improvement of bone and/or cartilagehealth so as to prevent, alleviate and/or treat bone and/or cartilagedisorders. Various embodiments are directed to the co-administration ofagents, such as tomatidine, resveratrol, rapamycin, etc. and aprobiotic, prebiotic and/or postbiotic to generate desired metabolitesto enhance the bone and cartilage health of an individual.

Aspects of the present invention are directed to achieving andmaintaining desired bone mass by modulating an individual’s microbiometo arrive at a balance between bone formation and bone resorption thatinvolves regulation of bone-forming cells (osteoblasts) andbone-resorbing cells (osteoclasts).

In addition to treating osteoporosis, modulating the balance betweenbone formation and bone resorption is important in conditionscharacterized by the need to increase bone formation, such as for bonefractures, periodontal diseases, metastatic bone diseases, osteolyticdiseases, frailty, reduced mobility, and osteoarthritis, where articularcartilage breaks down, leading to synovial membrane proliferation,sclerosis and thickness of subchondral bone, osteophyte formation atjoint margin, ligament laxity and muscle atrophy.

Various embodiments include the provision of probiotics for anindividual’s gut microbiome to promote the generation of desiredmetabolites from the bioconversion of dietary foods to produce shortchain fatty acids. The amount of daily probiotic, particularly one thatprimarily includes Bifidobacterium strains, for an individual ispreferably at least about 10^(13th) cfu per day. Moreover, as it isunderstood by those of skill in the art that certain bacteria possessbeta-glycosidase activity and/or esterase activity, namely bacteriabelonging to Lactobacillus and Bifidobacterium which inherentlypossessing both activities, the employment of either, but preferablyBifidobacterium strains to generate desired levels of SCFAs in anindividual’s gut microbiome, and particularly in one’s colon, is asignificant objective of many embodiments described herein.

In still further embodiments, in addition to increasing levels ofbutyrate provided to an individual so as to achieve the various benefitsas described herein, some embodiments include the provision oftributyrin, preferably via a fermented form of tributyrin. Tributyrin isan organic compound having the chemical formula C₁₅H₂₆O₆. Butyrate isthe conjugate base of butyric acid while tributyrin is a prodrug ofbutyric acid, with a preferred IUPAC name Propane-1,2,3-triyltributanoate. In such a manner, it is possible to provide individualswith a direct delivery of butyrate to the large and small intestine viacleaving by a lipase. Thus, while several embodiments of the presentinvention involve providing bacteria to an individual so as toproduce/generate SCFAs in their gut microbiome, namely butyrate, otherembodiments include an exogenous method of increasing butyrate in thegut of an individual that is independent of butyrate-producing bacteria,fiber requirements, etc. In certain preferred embodiments, at leastabout 300 mg of tributyrin is provided to an individual of the fermentedform of tributyrin, more preferably at a level of at least about 500 mg,and even more preferably by providing doses in the 500-1000 mg range. Ina similar manner, other embodiments involve the provision to anindividual of both tributyrin and tracetatin (e.g. acetates bound toglycerol) in combination. While not bound by theory, it is believed thata combination of acetate and butyrate, as well as other SCFAs, providehealth benefits to an individual. In preferred embodiments, methods ofthe present invention involve the provision of around a 1:3 ratio oftriacetin and tributyrin, e.g. (250 mg triacetin + 750 mg tributyrin)which is preferably orally delivered/administered to promote bone healthand to maintain optimal levels of SCFA levels during aging. In additionto butyrate, one of skill in the art will appreciate that in othervariants of the present invention, one may use sodium butyrate (having achemical formula Na(C₃H₇COO) to achieve various objectives, as it is thesodium salt of butyric acid. Such objectives include the inhibition ofproliferation, induction of differentiation, and/or induction of therepression of gene expression. Similarly, calcium magnesium butyrate canbe employed in other embodiments of the present invention as it is morestable than sodium butyrate and is less hygroscopic.

One will appreciate that this Summary of the Invention is not intendedto be all encompassing and that the scope of the invention nor itsvarious embodiments, let alone the most important ones, are necessarilyencompassed by the above description. One of skill in the art willappreciate that the entire disclosure, as well as the incorporatedreferences, figures, etc. will provide a basis for the scope of thepresent invention as it may be claimed now and in future applications.While embodiments of the invention have been illustrated and described,it is not intended that these embodiments illustrate and describe allpossible forms of the invention. Rather, the words used in thisspecification are words of description rather than limitation, and it isunderstood that various changes may be made without departing from thespirit and scope of the invention.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is an illustration of the effects of osteoporosis on human bones.

FIG. 2 is the chemical formula for xylitol.

FIG. 3 is the chemical formula for rapamycin.

FIG. 4 is the chemical formula for tomatidine.

DETAILED DESCRIPTION OF EMBODIMENTS OF THE PRESENT INVENTION

Osteoporosis is a disease associated with the aged. During aging a widespectrum of alterations in mitochondrial structure and function canoccur. Mutational damage accumulates over lifetime, in particularaffecting respiratory chain complexes, which results in theoverproduction of ROS and leads to mitochondrial dysfunction. Agingreveals that mitochondria become enlarged, have irregular shapes anddecrease in number. One aspect of the present invention is to bothprevent and treat osteoporosis. Certain embodiments are directed totreating and extending an individual’s healthspan to combat the ravagesof certain age related diseases, such as osteoporosis. In certainembodiments, the provision of effective amounts of tomatidine is used totreat or prevent osteoporosis.

Postmenopausal osteoporosis is initiated by estrogen withdrawal and ischaracterized mainly by over-activated osteoclastic bone resorption.While not bound by theory, it is believed that tomatidine inhibitsosteoclast formation in a dose-dependent manner and decreases theexpression of osteoclast marker genes. Tomatidine appears to attenuateosteoclast formation and function by modulating multiple pathways. Also,while not bound by theory, it is believed that tomatidine plays a rolein mitigating osteoporosis by inhibiting osteoclastogenesis and reducingestrogen deficiency-induced bone mass loss. Tomatidine also plays abiological role of mitigating apoptosis by inhibiting the expression ofp53.

There is increasing evidence that mitophagy is significantly impaired inseveral human pathologies including aging and age-related diseases suchas neurodegenerative disorders, cardiovascular pathologies, cancer andbone related diseases. Therapeutic interventions aiming at the inductionof mitophagy is believed to have the potency to ameliorate thesedysfunctions. As described herein, one therapeutic intervention is theadministration to an individual of a formulation that includes at leasttwo of tomatidine, xylitol and rapamycin to treat, prevent and to reducethe likelihood of osteoporosis.

Mitochondria originated from endosymbiotic proteobacteria and conferredsubstantial advantages for eukaryotic cells during evolution.Mitochondria play a critical role in ATP synthesis via oxidativephosphorylation (OXPHOS), β-oxidation regulating fatty acid metabolism,the synthesis of intermediate metabolites through the TCA cycle, as wellas calcium homeostasis. On the other hand, mitochondria are the centralorganelle controlling apoptotic cell death and the permeabilization ofthe mitochondrial outer membrane releases pro-apoptotic proteins such ascytochrome c, SMAC/DIABLO, ENDOG, OMI/HTR and AIF, which leads tocellular demise. Mitochondria are the major source of reactive oxygenspecies (ROS) which can oxidize proteins, lipids, and nucleic acids,inside (and outside) the mitochondria, leading to mitochondrialmalfunction and cellular damage. Mitochondria serve as an origin ofdamage associated molecular patterns (DAMP) and in particularmitochondrial DNA (mtDNA), which, once released from mitochondria intothe cytosol, can trigger inflammatory responses.

Autophagy is a conserved intracellular degradation mechanism thatremoves dangerous, unnecessary or dysfunctional cytoplasmic constituentsand invading microbes. Autophagic activity declines during aging, andautophagy is required for lifespan extension by caloric restriction orcaloric restriction mimetics (CRM) such as resveratrol, spermidine, andseveral chalcones. Mitophagy plays a key role in delaying aging andage-related disorders such as neurodegenerative disorders,cardiovascular pathologies, and cancer. One aspect of variousembodiments of the present invention is directed to therapeuticinterventions that harness mitophagy to treat age-related disorders.

The KEGG pathways involved in osteoporosis are associated withtomatidine-targeted genes, such pathways including chronic myeloidleukemia, B cell receptor signaling, cancer, bladder cancer, andprogesterone-mediated oocyte maturation. These pathways are alsoinvolved in the p53 signaling pathway and the MAPK signaling pathway. Itis believed that the downregulating of p53 expression may be protectivefor osteoporosis. Tomatidine administered to an individual who suffersfrom osteoporosis improves their lives by treating osteoporosis, withone of tomatidine’s mechanisms of action achieved by modulating p53.

Rapamycin, an allosteric inhibitor of mechanistic target of rapamycin(mTOR), prevents age-related conditions in humans. mTOR is a criticalnutrient sensor and has multiple downstream effects, including proteinsynthesis, and autophagy. Eliminating damaged mitochondria via mitophagyis believed to be a mechanism responsible for the beneficial effects ofrapamycin. Rapamycin enhances mitophagy.

Mitochondria are important for cellular life and death and mitophagy isthe mechanism to preserve for mitochondrial quality and quantitycontrol. Dysfunction of mitochondria is a characteristic of aging andage-related disease and mitophagy counterbalances age-relatedpathological conditions. Thus, one aspect of the present invention isdirected to stimulation of mitochondrial turnover by enhancing mitophagyto treat and prevent (or delay) age-related diseases and to extendhealthspans and lifespans.

The positive effects of tomatidine on muscle mass are accompanied byincreased strength and exercise capacity, as well as increased specificforce, which shows that tomatidine may have a greater effect on strengththan muscle mass. Aspects of the present invention are directed to boththe avoidance of muscle atrophy while also reducing the likelihood ofosteoporosis.

As used herein, the terms “effective amount” and “amount effective”refer to an amount that is sufficient to achieve the desired result orto influence an undesired condition. For example, a “therapeuticallyeffective amount” refers to an amount that is sufficient to achieve thedesired therapeutic result or to have an effect on undesired symptoms,but is generally insufficient to cause adverse side effects. Thespecific therapeutically effective dose level for any particular patientwill depend upon a variety of factors including the disorder beingtreated and the severity of the disorder; the specific compositionemployed; the age, body weight, general health, sex and diet of thepatient; the time of administration; the route of administration; therate of excretion of the specific compound employed; the duration of thetreatment; drugs used in combination or coincidental with the specificcompound employed and like factors well known in the medical arts. Forexample, it is well within the skill of the art to start doses of acompound at levels lower than those required to achieve the desiredtherapeutic effect and to gradually increase the dosage until thedesired effect is achieved. If desired, the effective daily dose can bedivided into multiple doses for purposes of administration.Consequently, single dose compositions can contain such amounts orsubmultiples thereof to make up the daily dose. The dosage can beadjusted by the individual physician in the event of anycontraindications. Dosage can vary, and can be administered in one ormore dose administrations daily, for one or several days. Guidance canbe found in the literature for appropriate dosages for given classes ofpharmaceutical products, such as xylitol, rapamycin and tomatidine. Infurther various aspects, a preparation can be administered in a“prophylactically effective amount”; that is, an amount effective forprevention of a disease or condition. In various embodiments, aneffective amount of rapamycin may be 50 to 250 micrograms; or between0.1% to 20% of rapamycin based on total weight of the formulation; or atleast 0.1 mg of rapamycin; or a dose of rapamycin in the range of 1mg/day to 5 mg/day, and in other embodiments, in the range from about0.01 .mu.g/day to about 50 .mu.g/day. In certain embodiments, theeffective amount of tomatidine is at least 10 micro-mole of tomatidine;and at least 200 mg of xylitol or at least 0.2% xylitol by weight.

Tomatidine is present in high amounts in the unripe green tomato and inmuch lower amounts in the ripe red tomato. This is consistent with arole for tomatidine in protecting the unripe tomato against consumption,with the reduction in tomatidine levels in the ripe fruit then enablingconsumption of the fruit and dispersal of the seeds by the consumer.Moderate amounts of tomatidine can activate adaptive cellular stressresponses in muscle cells and thus, counteract age-related dysfunctionand degeneration.

While not bound by theory, it is believed that such administration oftomatidine extends the lifespan and healthspan of humans and othermammals by inducing mitochondrial hormesis via the induction of ROSproduction. This further entails the activation of certain cellular andantioxidant pathways, including the SKN-⅟Nrf2 pathway, which results inincreased mitophagy. The selective removal of damaged or dysfunctionalmitochondria by mitochondrial autophagy, termed mitophagy, is believedto be a feature of a treatment to extend an individual’s lifespan in asafe and effective manner. Mitophagy modulates bioenergetics andsurvival in various diseases by reducing redox and damage. Impairedmitophagy occurs in physiological aging, as well as in certain diseases,such as sarcopenia and also believed to be present in cachexia. Incertain embodiments, the administration or delivery of certain noxiouschemicals are believed to counteract aging and age-related disease byinducing adaptive hormetic stress responses in cells. In otherembodiments, the inclusion of rapamycin administration is employed toimprove the healthspan of humans as it is further related to mitophagy.The methods and systems as set forth herein are directed to theextension of human life span in a fashion that promotes healthy agingand counteracts disease processes related to age-related disease,including but not limited to osteoporosis.

Tomatidine administration as described in the present specification isbelieved to contribute to a delay in the physiological aspects of aging,and thus, is able to prevent, treat and reduce the likelihood ofosteoporosis. For example, it is believed that tomatidine increasesmitochondria DNA content and muscle fitness and lowers adiposity, aswell as decreases skeletal muscle atrophy. While not bound by theory, itis believed that the administration of tomatidine maintains homeostasisby modulating mitochondrial biogenesis and induces mild oxidativestress, which activates the above referenced pathways to inducemitophagy. The amount of tomatidine administered is believed to beimportant to achieve its desired age fighting effects, with at leastabout 10 micro-mole, and more beneficially with between about 25micro-mole and 50 micro-mole being preferred. Moreover, administrationof tomatidine is believed to increase the production in an individual ofamounts of certain amino acids, such as free amino acids of leucine,threonine, tryptophan, arginine, histidine, valine, isoleucine, andmethionine. Such administration is also believed to affect ROSregulation and metabolism. As aging is known to negatively affectmitochondrial quality and biogenesis, the use of tomatidine to enhancemitophagy can be employed to reduce the amount of neurodegeneration andcellular dysfunction of cell metabolism, especially by inducing anincrease in Nrf2/ARE reporter activity. Upon activation by ROS, Nrf2translocates from the cytoplasm of a cell to the nucleus, where it bindsto the ARE region to transcriptionally activate genes encodingantioxidant proteins. Thus, tomatidine administration activates theNrf2-ARE pathway by inducing cells to increase levels of ROS, resultingin the contribution to mitophagy induction. While not bound by theory,it is also believed that administration of tomatidine as describedherein acts via multiple stress response pathways, such as, in additionto the Nrf2 pathway referenced above, through the activation of themitochondrial unfolded protein response (UPR mt). Compromisedmitochondrial quality and function is related to pathological aging anddisease and the accumulation of damaged mitochondria within cellstriggers apoptosis, inflammation and cell senescence. Sarcopenia isobserved in aging individuals, with almost 25% of those over 60 yearsold experiencing the same, rising to over 50% by the age of 80.Tomatidine is believed to preserve muscle function during aging andtherefore extends lifespan by improving mitochondrial quality byreducing muscle atrophy. Sarcopenia is therefore common in aging and isassociated with the deterioration of muscle fiber cells and withinfiltration of adipocytes and inflammatory immune cells, impairing thegeneration of new myocytes. In various embodiments of the presentinvention, the employment of tomatidine is not resultant from effects onmuscle stem cells or immune cells, but rather, is directed to the effectthat tomatidine has in influencing the muscle cells themselves as it isbelieved that the mechanism of action is directed to processes occurringwithin skeletal muscle fiber cells.

Various aspects of the present invention are directed to the inductionof mitophagy by the administration of tomatidine, especially via themicrobiome cells of an individual as otherwise described herein, so asto enhance the quality of the cellular mitochondrial pool and/ormitochondrial biogenesis. Support for this theory of action can befound, for example, in studies of premature aging disease, such asHutchinson-Gilford progeria syndrome, caused by a mutation of thenuclear architectural proteins lamin A and C. Such patients showedprofound growth delay and premature aging phenotypes, including cardiacmuscle and skeletal muscle pathologies. It is known that Nrf2 activitycontributes to premature aging and that activation of the Nrf2 pathwayameliorates such disease. One aspect of the present invention istherefore directed to the administration of tomatidine, in particular asdescribed herein via expression by or in conjunction with variousbacteria in an individual’s microbiome, so that it triggers mitophagyand induces Nrf2 activation. A signaling role for ROS in the stimulationof mitophagy in cells under mild stress supports the use of tomatidineas described herein, as moderately elevated ROS levels have been seen asinducing mitophagy, which has the effect of clearing aged ordysfunctional mitochondria. If ROS levels are too high, however, or ifmitophagy is compromised, mitochondrial dysfunction becomes exacerbated,demonstrating that ROS levels have a dynamic role in health and agingdisease. Employment of tomatidine to achieve a moderate elevation of ROSlevels is therefore one objective of various embodiments of the presentinvention, but with care not to achieve excessive ROS levels, thusaccomplishing the desired goal of enhancing cellular stress resistancein a manner that is disease protective. Tomatidine is thereforepreferably administered in effective amounts that induce a moderateincrease in ROS levels that is necessary to trigger mitophagy withoutdemonstrating mitochondrial dysfunction.

Tomatidine is not believed to have significant anti-microbial effects,at least when used alone. When co-administered with other compounds,however, it is believed that there is a synergistic effect andtherefore, tomatidine is viewed as an antibiotic potentiator when usedwith ampicillin, etc. Preferably, tomatidine, in certain embodiments isused at a concentration of about 200 micro grams per mL. Thus, inseveral embodiments, the use of tomatidine administration in anindividual is employed to synergistically enhance the action of variousantibiotics against certain bacteria. Such synergistic effects arebelieved to be also accomplished when tomatidineexpression/administration in an individual is coupled of theco-administration with at least one of the following: p53 protein,rapamycin, resveratrol, metformin, spermidine, xylitol, glucosamine andmethylene blue.

Short-chain fatty acid production by commensal bacteria is important inregulating the immune system in the gut. Butyrate plays a direct role ininducing the differentiation of regulatory T cells and suppressingimmune responses associated with inflammation. Butyrate is normallyproduced by microbial fermentation of dietary fiber and plays a centralrole in maintaining colonic epithelial cell homeostasis and barrierfunction. Use of such modified bacteria, especially those modified viaCRISPR-Cas systems, provides a way to generate a desired therapeuticeffect in a manner that lowers the safety issues associated withsystemic exposure. Importantly, the increase in butyrate and otherSCFA’s should be accomplished only if an individual’s gut barrierfunction has not been compromised as high systemic concentrations ofpropionate and butyrate may otherwise lead to adverse effects, such asincreased serum levels of SCFAs due to the enhanced “leak” of the gutbarrier.

Resveratrol (3,4′,5-trihydroxystilbene; C.sub.14H.sub.12O.sub.3) is apolyphenolic phytoalexin found in grapes, berries, peanuts, and wines.Resveratrol has been viewed as an antioxidant, anti-inflammatory,anti-apoptotic, and anticancer agent. Moreover, it has been reportedthat resveratrol modulates mitochondrial function, redox biology, anddynamics in both in vitro and in vivo experimental models. Resveratrolalso attenuates mitochondrial impairment induced by certain stressors.Resveratrol upregulates, for example, mitochondria-located antioxidantenzymes, decreasing the production of reactive species by theseorganelles. Resveratrol also triggers mitochondrial biogenesis,ameliorating the mitochondria-related bioenergetics status in mammaliancells. Brain cells (both neuronal and glial) are susceptible tomitochondrial dysfunction due to their high demand for adenosinetriphosphate (ATP). Additionally, brain cells consume oxygen (O.sub.2)at very high rates, leading to a proportionally high mitochondrialproduction of reactive species. One aspect of various embodiments of thepresent invention is the maintenance of mitochondrial function invarious cell types to address degenerative diseases, which involvemitochondrial impairment and increased generation of reactive species,leading, for example, to neuroinflammation and cell death. The mechanismby which resveratrol protects mitochondrial function and dynamics is notcompletely understood, but it is known that resveratrol is able toinduce cytotoxicity depending on its dosage. Resveratrol produced by themicrobiome of an individual (or precursors thereof) can be employed toimprove the dysregulation of the gut microbiota induced by a high-fatdiet, as it results in increasing the ratio of Bacteroides-to-Firmicutesand also increases the growth of Lactobacillus acidophilus andBifidobacterium in humans. It is believed that resveratrol modifies theintracellular environment by changing the oxidizing milieu into areducing milieu and upregulates intracellular glutathione, potentiatinga signal transduction cascade that results in mitophagy, and thus pavesthe way to an anti-aging environment.

Mammalian/mechanistic target of rapamycin (mTOR) is an intracellularprotein complex that is responsive to both growth factors and nutrientavailability, and which also impacts mitochondrial function. It iscomprised of the TOR kinase--known as mTOR in mammals. The TOR signalingpathway is highly conserved in eukaryotes and is functionally defined asthe target of the highly-specific antifungal, rapamycin. mTOR and agingappear to have co-evolved, suggesting that cancer is inexorably linkedto fundamental aspects of life. Rapamycin can be employed, viaproduction by or used in conjunction with an individual’s microbiome, toachieve the objective of delaying the effects of aging and thus, reducediseases associated with aging, including osteoporosis. Age-associateddiseases interface with TOR and its signaling systems, and thus,employment of rapamycin (alone or in concert with the various otheragents described herein) provides the ability to target both aging andits associated diseases, including osteoporosis.

In certain embodiments, precursors of one of xylitol, rapamycin andtomatidine are administered via an individual’s own microbiome as a wayto deliver a therapeutic treatment that works on everyone despite thedistinct and acknowledged differences between an individual’smicrobiome. The differences of each individual’s microbiome works infavor of this approach as delivery of rapamycin via one’s own microbiomeis naturally customed tailored as focusing on modification of anindividual’s microbiome provides desired anti-aging agents whilemaintaining the distinct character of an individual’s microbiome. Agingis therefore possible to treat in a personalized way by taking intoaccount the individual’s unique microbiome. The present inventionprovides a way to tailor preventive measures and treatments to differentindividuals. Mechanical loading plays a major role in the regulation ofskeletal muscle mass, and the maintenance of muscle mass profoundlyinfluences health and quality of life. Signaling by themammalian/mechanistic target of rapamycin (mTOR) is a key component ofthe mechanotransduction pathway. Employment of an individual’smicrobiome to administer effective amounts of rapamycin to theindividual is one way in which to modulate mTOR signaling, thusaffecting muscle mass and associated bone density.

A variety of stimuli, such as nutrients, growth factors, and mechanicalloading, can regulate protein synthesis in skeletal muscle. Theregulation of translation initiation by these stimuli is mediated bymTOR, which exists in at least two characteristically distinctcomplexes; a) the rapamycin-sensitive mTOR complex 1 (mTORC1), and b)the rapamycin-insensitive mTOR complex 2 (mTORC2). The control oftranslation initiation by mTOR is one of the key steps for theregulation of protein synthesis in skeletal muscle. Rapamycin, a highlyspecific inhibitor of mTOR signaling, can prevent protein synthesisinduced by various forms of mechanical loading such as resistanceexercise. Rapamycin can prevent chronic mechanical overload-inducedincreases in fiber size (i.e., hypertrophy). Rapamycin-sensitive mTORsignaling plays a central role in the regulation of protein synthesisand muscle mass during periods of increased mechanical loading. mTOR isthe rapamycin-sensitive element that confers mechanically induced musclegrowth. Rapamycin exhibits growth inhibitory effects. mTOR, withinskeletal muscle cells, is the primary rapamycin-sensitive element thatconfers a mechanically-induced hypertrophic response. The targeting ofmTOR signaling is therefore critical in various methods directed to theprevention of muscle atrophy. mTOR is a crucial component in themechanotransduction pathway that promotes muscle growth. mTOR signalinginduces skeletal muscle growth via a rapamycin-sensitive mechanism.Mechanical loading activates mTOR signaling and muscle growth through aunique mechanism but the identity of this mechanism remains unclear.

Administration of formulations that include at least one of and morepreferably two of the following: xylitol, tomatidine and rapamycin, andespecially when an individual’s microbiome is modified to achieveincreased amounts of butyrate production (as compared to pre-treatmentlevels) can therefore mitigate osteoporosis and therefore treat, preventand/or reduce the likelihood of the disease.

Skeletal muscles consume a lot of energy (i.e., ATP) during every cyclicinteraction between actin and myosin, and importantly, these activemuscles comprise approximately 45% of total body mass. As mitochondriaare the source of ATP in humans and in view of the importance ofmitophagy as described herein, the link between rapamycin and tomatidinewith mitochondria and the retention of muscle mass of an individual canbe discerned.

Skeletal muscles can also play a critical role in the regulation ofwhole-body energy metabolism. Skeletal muscle mass is inverselyassociated with several metabolic disorders such as obesity, diabetes,and metabolic syndromes. Thus, the maintenance of skeletal muscle massis not only keeping human bodies physically functional, but alsometabolically healthy. As skeletal muscle functions are directlyassociated with its mass, and thus, the maintenance of skeletal musclemass will contribute significantly to health and quality of life.Skeletal muscle mass is reduced with aging and both sedentary and activeadults will lose up to 30-40% of their muscle mass, which is directlyrelated to and is associated with disability, loss of independence, anincreased risk of morbidity and mortality. While it is known thatskeletal muscle mass can be increased by mechanical loading/stimuli(e.g., mechanical overload, etc.) in many individuals, there areproblems with achieving such stimuli, including the simple humanpropensity for the avoidance of exercise. The present invention, invarious aspects, provides an alternative, as well as a co-treatment, forthose individuals who cannot or who do not engage in mechanicalloading/stimuli to preserve their muscle mass as they age, thuspreventing muscle atrophy.

It has been observed that caloric restriction in a variety oforganisms--including mice, flies, worms, and yeast--achieves an extendedlife span and activates cellular protection pathways. In humans,however, caloric restriction often results in a weakening of the immunesystem. In any event, it is a largely impracticable way to realisticallyachieve the goals of a long and healthy life. The present inventionprovides a better way. A comparison of stools from aged vs. young humansreveals that older frail folks had lower levels of short-chain fattyacids, which the microbes in our guts normally make from dietary fiber.These short-chain fatty acids, including acetate, butyrate, andpropionate, are an important energy source for the colon. Frail subjectsalso had gut microbiomes depleted in species of bacteria that could dothis chemical conversion. It has also been observed that cancerous cellsoften become senescent and secrete chemical messages to nearby cells,all the while ceasing division. When enough senescent cells accumulate,their combined chemical cocktail results in a variety of age-relatedproblems, including osteoporosis.

Mitochondria are critical in understanding aging, as demonstrated bysome of the first genes found to extend worm lifetimes coding fordysfunctional proteins in mitochondria. The shortening of telomeres isalso associated with aging, but attempts to use telomerase to helprebuild shortened ends often results in cancer. For most of humanevolutionary history, a human’s life span was extremely short andtherefore, few died of old age diseases, such as cancer or heartdisease. Evolution optimized most human traits so we could survive longenough to produce offspring. In the late 1990s, researchers discoveredthat simple mutations in single genes could double, triple, and evenmore radically increase the life span of worms and single gene mutationswere also found that could extend life span in fruit flies and mice andother organisms. Some therefore believe that because simple geneticinterventions can extend lifetimes and healthspans, targeting such geneswill result in addressing aging. But such a route entails undesiredhuman genetic manipulation. The present invention avoids such a dramatictactic and achieves the desired and long-sought anti-aging objective viamanipulation of an individual’s microbiome, rather than their human DNA.

The process of oxidative phosphorylation for ATP generation inmitochondria is the main source of reactive oxygen species (ROS) withinthe cell (about 90% of total ROS in cells). The limited repair capacityof mitochondrial DNA (mtDNA) makes them particularly vulnerable toaccumulation of damages, with mutations in mtDNA resulting in increasedROS production, which causes diverse damages in the cells. The ROSvicious cycle is believed to account for an exponential increase inoxidative damage during aging. Senescent cells also increase with ageand have been found at sites of age-related pathologies. Chronicallyactive p53 both promotes cellular senescence and accelerates agingphenotypes.

One prominent response of cells to tomatidine is induction of mitophagy,which preserves cellular function during aging. Mitochondrialdysfunction and defective mitophagy are implicated in the etiology ofseveral major age-related diseases. Certain aspects of the presentinvention are directed to alterations of an individual’s microbiota interms of the particular composition, diversity and functional featuresof the intestinal microbiota to combat chronic inflammation and variousaging-associated pathologies. Such modification of an individual’smicrobiome, whether it be skin, oral, vaginal, but especially intestinalgut microbiota, is performed in a manner to favorably enhanceantioxidant activity, improve immune homeostasis, suppress chronicinflammation, and regulate fat metabolism.

To comply with written description and enablement requirements, allreferences cited herein, including but not limited to published andunpublished applications, patents, and literature references, areincorporated herein by reference in their entirety and are hereby made apart of this specification. To the extent publications and patents orpatent applications incorporated by reference contradict the disclosurecontained in the specification, the specification is intended tosupersede and/or take precedence over any such contradictory material.Incorporated herein by this reference are the following U.S. Pat.Publications: 20170079947 to Richards; 20140296139 to Cohen et al.;20160175327 to Adams et. al.; 20100081681 to Blagosklonny and20120283269 to Blagosklonny; U.S. Pat. Publication Nos. 20140030332 toBaron, et al., 20070123448 to Kaplan et al.; 20160000841 to Yamamoto, etal.; 20160095316 to Goodman et al.; 20160158294 to Von Maltzahn;20140294915 to Kovarik; U.S. Pat. No. 8,034,601 to Boileau et al.;20130225440 to Freidman, et al., 20150071957 to Kelly et al.,20160151428 to Bryann et al.; 20160199424 to Berry et al.; 20160069921to Holmes, et al.; 20160000754 to Stamets; U.S. Pat. No. 9,044,420 toDubensky, Jr, et al.; 20160120915 to Blaser et. al.; 2014/0349405 toSontheimer; 2014/0377278 to Elinav; 2014/0045744 to Gordon; 2013/0259834to Klaenhammer; 2013/0157876 to Lynch; 2012/0276143 to O′Mahony;2015/0064138 to Lu; 2009/0205083 to Gupta et al.; 201/50132263 to Liu;and 2014/0068797 to Doudna; 2014/0255351 to Berstad et al.; 2015/0086581to Li; PCT/US2014/036849 and WO 2013026000 to Bryann; U.S. Pat.Publication No. 2015/0190435 to Henn; 2012/0142548 to Corsi et al.; U.S.Pat. Nos. 6,287,610, 6,569,474, U.S.2002/0009520, U.S.2003/0206995,U.S.2007/0054008; and U.S. Pat. No. 8,349,313 to Smith; U.S. Pat. No.9,011,834 to McKenzie; 20150004130 to Faber et. al, 20160206666 to Falb;20160206668 to Kort et. al; and WO2015069682A2 to Asesvelt, et. al.;20160199424 to Berry et al.; 20130326645 to Cost et al.; 2012/0276149 toLittman; and U.S. Pat. No. 9,314,489 to Kelly et. al.; 20160243132 toAdams, et. al.; 9,549,842 to Kovarik; 20200032224 to SCHAEFER et. al. ;20170014341 To Armer, et. al. and US Pat. No. 10,683,323 to Prakash, et.al., US 20230106721 to Catania, et. al., US 20070072797 to Robinson, et.al. ;US Pat. No. 11,504,387 to Horcajada et. al. ; US 20230106721 toCatania, et. al

Proper functioning of mitochondria, as the central organelle formetabolism and other cell signaling pathways, is required to maintainrapid growth and proliferation of cancer cells since tumor cells devoidof mitochondria grow very slowly. Increased amounts of lactate not onlyblocks acetyl-CoA metabolism in mitochondria, but also reducesmitochondrial biogenesis as well as oxygen consumption. Tumorsuppressor, P53, plays an important role in promoting cell death as itis activated via a ROS-dependent pathway and leads to apoptosis incancer. Inhibited cell growth and increased apoptosis in cancer by P53activation are also regulated by miRNA or SIRT2 dependent pathways.Lactate-producing cancer cells are characterized by increased aerobicglycolysis and excessive lactate formation, a phenomenon described byOtto Warburg 93 years ago, which still remains unexplained. In 1923,Otto Warburg observed that cancer cells were characterized byaccelerated glycolysis and excessive lactate formation even under fullyoxygenated conditions. His discovery was subsequently named the “WarburgEffect’. While the Warburg Effect is a hallmark of cancer, the study ofcancer cell metabolism was diverted when investigators began to employgenomic techniques to better understand cancer biology. The cure forcancer through gene-based research, however, has yet to come tofruition, and the role of the Warburg Effect in cancer growth andcarcinogenesis is still a mystery. One aspect of the present inventionrelates to the production of various agents by an individual’smicrobiome, including the use of lactobacterium that produce lactate.There has been a recent renewal of interest in lactate as a player incancer as lactate is an obligatory product of glycolysis, an importantmetabolic fuel energy source, and an important signaling molecule. Inlactagenic cancers, there is observed a decrease in mitochondrialfunction. Lactate production constantly occurs in skeletal muscles aslactate is the obligatory product of glycolysis. The rate of lactateproduction is greatly enhanced in working skeletal muscles and thus, ithas been observed that during high-intensity exercise, working musclesdisplay some of the same metabolic characteristics as do cancer cells.Certain aspects of the present invention are therefore directed to theemployment of lactobacterium via introduction into an individual’smicrobiome, such that the levels of lactate can be achieved to addresslactate metabolism. Damaged mitochondria are responsible for increasedproduction of reactive oxygen species, metabolic inflexibility, andinflammation.

A number of compounds have been found to stimulate autophagy, includingrapamycin, resveratrol, metformin, spermidine, and glucosamine. mTOR,the mammalian target of rapamycin, is considered to be a majorcheckpoint in a pathway linking the cellular nutritional state with thelevel of ongoing autophagy. Mitochondria can be selectively targeted fordegradation via macroautophagy (mitophagy). Induction of autophagy is animportant homoeostatic mechanism that is disrupted in dystrophicmuscles. Autophagy promotes osteogenic differentiation of human bonemarrow mesenchymal stem cells. Rapamycin is a well-characterizedautophagy stimulator. The mTOR pathway is involved in promoting anabolicprocesses, ribosome biogenesis, protein synthesis and many cellularpathways, inhibiting cell stress responsive pathways, and proteindegradation by autophagy. Inhibiting mTOR with agents such as rapamycinretards protein synthesis and enhances cell stress responsive pathways,such as autophagy.

Treatment with rapamycin and rapalogs (rapamycin analogues) and the roleof mTOR signaling via the mTORC1 complex on osteoclast, osteoblast, andosteocyte differentiation and function is generally considered to be alargely bone-sparing drug which may improve compromised bone quality.One aspect of the present invention relates to an individual’s treatmentwith rapamycin to restore osteoblast differentiation and bone volume andto reduce the severity of senile osteoporosis. It is believed thatrapamycin’s stimulation of autophagy provides a clinical approach in thetreatment of osteoporosis. Rapamycin-induced autophagy improves bonefracture healing and has beneficial effects on the trabecularcompartment of long bones. Certain embodiments employ a dose ofrapamycin in the range of 1 mg/day to 5 mg/day, and in otherembodiments, in the range from about 0.01 .mu.g/day to about 50.mu.g/day.

Autophagy is a cellular process that degrades damaged proteins andmitochondria. The failure of this process in the elderly to effectivelyrid the body of such damaged proteins and organelles leads to theage-associated malfunctions of many biological processes. Mitochondriais an intracellular signaling organelle that communicates with the restof the body to regulate metabolism and cell fate and thus, manipulationof mitochondria is believed to be involved in addressing a majority ofage-related diseases, including osteoporosis. Mitochondria have theirown small collection of genes, which were once thought to play onlyminor roles within cells but now appear to have important functionsthroughout the body. Humanin and MOTS-c, hormones that appear to havesignificant roles in metabolism and diseases of aging, are unlike mostother proteins, as they are encoded in mitochondria, rather than in thecell’s nucleus where most genes are contained. Aged mammals contain highquantities of oxidized lipids and proteins, as well as damaged/mutatedDNA, particularly in the mitochondrial genome. A major effect ofmitochondrial dysfunction is an inappropriately high generation of ROSand proton leakage, resulting in lowering of ATP production in relationto electron input from metabolism. Leaked ROS and protons cause damageto a wide range of macromolecules, including enzymes, nucleic acids andmembrane lipids within and beyond mitochondria and thus are consistentwith the inflammation theory of aging as being proximal eventstriggering the production of pro-inflammatory cytokines. Free radicalscan damage the mitochondrial inner membrane, creating a positivefeedback-loop for increased free-radical creation. Induction of ROSgenerates mtDNA mutations, in turn leading to a defective respiratorychain. Defective respiratory chain generates even more ROS and generatesa vicious cycle. One aspect of the present invention is directed to atherapeutic approach that employs autophagy, and preferably mitophagy,to reduce muscle damage and wasting and to also reduce the likelihood ofosteporosis. In certain embodiments, the use of the described treatmentcan be employed to combat human muscular dystrophy (DMD). Autophagy isknown to be defective in human muscular dystrophy and such defectcontributes to the pathogenesis of the disease.

Mitochondria are the cell’s chief energy producing organelles. A cellcan contain hundreds of mitochondria, the DNA of which encodes a subsetof mitochondrial RNA and proteins. The mitochondrial theory of agingproposes that mutations progressively accumulate within themitochondrial DNA. The consequences are predicted to be particularlydire for non-proliferative cells in organs that have a minimal capacityto regenerate (quiescent tissues), such as the heart and brain. Theactivity of master regulators of mitochondrial function and numberdiminishes with aging, further contributing to mitochondrial deficiency.For example, with age, telomere damage in the nucleus triggers theactivation of p53, which can have different effects. p53 is a gene thatdirects damaged cells to stop reproducing or die. The gene helps preventcancer in younger people but may be partly responsible for aging byimpairing the body’s ability to renew deteriorating tissues. Prominentage-related diseases are further believed to be related to hormesis, inwhich biological stress, such as exercise, elicits a biological responsethat confers resistance to greater amounts of stress. This effect is dueto increased formation of free radicals within the mitochondria causinga secondary induction of increased antioxidant defense capacity.Mitochondria are central to metabolic processes and are is involvedenergy production, programmed cell death, reactive oxygen species (ROS)generation, and is implicated in various stages of major diseasesincluding cancer, diabetes, neurodegenerative diseases, and aging. Inproliferative cells, p53 halts both cell growth and DNA replication,potentially causing apoptotic cell death. p53 also represses theexpression of PGC-1 in mitochondria, reducing the function and number ofthese organelles, and so leading to age-related dysfunction ofmitochondrion-rich, quiescent tissues. The mitochondrial derangementsdriven by loss of PGC-1 activity may independently lower the thresholdfor the generation of toxic intermediates such as reactive oxygenspecies (ROS), which damage mitochondrial DNA, thus setting up a viciouscycle of further mitochondrial dysfunction. Mitochondria-derived humaninshares 92-95% identity with several nuclear-encoded cDNAs. A 24 aminoacid peptide, known as humanin (HN), is highly conserved among species(between 90-100% homology), including lower organisms. Unlike most otherproteins, humanin and MOTS-c are encoded in mitochondria, the structurewithin cells that produces energy from food, instead of in the cell’snucleus where most genes are contained. As humanin and MOTS-c arehormones that have significant roles in metabolism and the diseases ofaging, the regulation of the same via production of the same via anindividual’s microbiome forms one aspect of various embodiments of thepresent invention. Similarly, the SHLP family of compounds that areexpressed by mitochondria play a major role in the intracellularsignaling and communication to regulate metabolism and cell fate andthus are important in addressing methods for combating aging.

Certain embodiments of the present invention are directed to bacterialproduction by genetically modified bacteria to produce or to be used inconjunction with one of xylitol, tomatidine and/or rapamycin, especiallythe precursors thereof such that biosynthesis of these agents can beprovided to those in need., e.g. those suffering from osteoporosis.Bacteria that may produce xylitol include Corynebacterium sp.,Enterobacterium liquefaciens, Serratia marcescens, Bacillus coagulansand Mycobacterium smegmatis. Certain embodiments of the presentinvention involve the production of xylitol by genetically modifiedbacteria, including those listed above, preferably using CRISPR systemsto include genes responsible for xylitol production in yeasts, such asPichia stipitis. The genes of yeasts that encode for xylitol productionare well known by those of skill in the art. Incorporation of thesegenes into suitable bacterial vectors is within the skill of those inthe art. For example, deletion of the Escherichia coli xylulokinase gene(xylb) is essential for achieving high xylitol titers fromxylitol-producing E. coli strains growing on glucose in the presence ofxylose. The yeast Pichia stipitis naturally produces xylitol.Replacement of xylB with XYL3 results in drastically enhanced xylitoltiters from E. coli strains co-expressing xylose reductase during growthon xylose. Biological conversion of xylitol using microorganisms isachieved in some embodiments via using genetically modifiedmicroorganisms capable of converting readily available carbon sources,such as D-glucose, into xylitol.

In certain embodiments, in addition to xylitol, tomatidine and/orrapamycin, the formulation includes at least one calcium source.According to a particular embodiment, the calcium source is any compoundcontaining calcium, including salt complexes, solubilized species, andother forms of calcium. Non-limiting examples of calcium sources includeamino acid chelated calcium, calcium carbonate, calcium oxide, calciumhydroxide, calcium sulfate, calcium chloride, calcium phosphate, calciumhydrogen phosphate, calcium dihydrogen phosphate, calcium citrate,calcium malate, calcium citrate malate, calcium gluconate, calciumtartrate, calcium lactate, solubilized species thereof, and combinationsthereof. In still other embodiments, the formulation includes amagnesium source. The magnesium source is any compound containingmagnesium, including salt complexes, solubilized species, and otherforms of magnesium. Non-limiting examples of magnesium sources includemagnesium chloride, magnesium citrate, magnesium gluceptate, magnesiumgluconate, magnesium lactate, magnesium hydroxide, magnesium picolate,magnesium sulfate, solubilized species thereof, and mixtures thereof. Inanother particular embodiment, the magnesium source comprises an aminoacid chelated or creatine chelated magnesium. In still otherembodiments, the formulation includes one or more of vitamins D, C, K,their precursors and/or beta-carotene and combinations thereof.

Yet further embodiments include in the formulation at least one plantextract selected from the group that include species of the genusTaraxacum and Amelanchier, as disclosed in U.S. Pat. Publication No.2005/0106215, and species of the genus Lindera, Artemisia, Acorus,Carthamus, Carum, Cnidium, Curcuma, Cyperus, Juniperus, Prunus, Iris,Cichorium, Dodonaea, Epimedium, Erigonoum, Soya, Mentha, Ocimum, thymus,Tanacetum, Plantago, Spearmint, Bixa, Vitis, Rosemarinus, Rhus, andAnethum.

It has been observed by the present inventor that producing Haikuresembles the generation of a patent claim. There is requisitestructure, a need to communicate substance and an ethereal quality ofunderstanding. As one of skill in the art of both biology and haiku willappreciate with respect to osteoporosis:

Osteoporosis ...is more than just a gut feeling Tomatidine cures.

While specific embodiments and applications of the present inventionhave been described, it is to be understood that the invention is notlimited to the precise configuration and components disclosed herein.Various modifications, changes, and variations which will be apparent tothose skilled in the art may be made in the arrangement, operation, anddetails of the methods and systems of the present invention disclosedherein without departing from the spirit and scope of the invention.Those skilled in the art will appreciate that the conception upon whichthis disclosure is based, may readily be utilized as a basis fordesigning of other methods and systems for carrying out the severalpurposes of the present invention. It is important, therefore, that theclaims be regarded as including any such equivalent construction insofaras they do not depart from the spirit and scope of the presentinvention.

What is claimed is:
 1. A method for reducing the likelihood ofdeveloping osteoporosis in an individual human being, comprising:providing via oral administration a population of beneficial bacteriathat produce butyrate, said beneficial bacteria encapsulated in a shellthat protects said beneficial bacteria from contact with an individual’sstomach acid, said beneficial bacterial comprising at least one ofCoprococcus, Roseburia, Bifidobacterium, Faecalibacterium prausnitziiand Akkermansia muciniphila; and administering at least 6 grams per dayof fiber to the individual to maintain a therapeutically effectiveamount of the beneficial bacteria in the gut of the individual humanbeing.
 2. The method as set forth in claim 1, wherein the individual isa postmenopausal woman.
 3. The method as set forth in claim 1, furthercomprising providing to the individual at least about 300 mg oftributyrin.
 4. The method as set forth in claim 1, further comprisingreducing the number of bacteria in the individual using a clusteredregularly interspaced short palindromic repeats (CRISPR) CRISPRassociated protein (Cas) system or a CRISPR from Prevotella andFrancisella 1 (Cpf1) system.
 5. The method as set forth in claim 1,wherein said beneficial bacteria have been modified by using a clusteredregularly interspaced short palindromic repeats (CRISPR) CRISPRassociated protein (Cas) system or a CRISPR from Prevotella andFrancisella 1(Cpf1) system.
 6. The method of claim 1, further comprisingadministering to the individual at least 10 micro-mole of tomatidine. 7.The method as set forth in claim 1, further comprising administering oneof rapamycin and resveratrol to the individual.
 8. A method for reducingthe likelihood of developing osteoporosis in an individual human being,comprising: providing to an individual a population of beneficialbacteria selected from the group consisting of bacteria that produce abutyrate concentration in the individual’s intestinal lumen of between 1and 10 mmol/l of food content present in the individual’s intestinallumen; and administering at least 6 grams per day of fiber to theindividual to maintain a therapeutically effective amount of thebeneficial bacteria in the gut of the individual human being.
 9. Themethod as set forth in claim 8, wherein the beneficial bacteria compriseFaecalibacterium prausnitzii.
 10. The method as set forth in claim 8,wherein the beneficial bacteria comprise Akkermansia muciniphila. 11.The method as set forth in claim 8, further comprising selectivelyreducing in the individual’s gut microbiome bacteria selected from thegroup consisting of Actinomyces, Eggerthella, and Clostridium ClusterXIVa.
 12. The method of claim 8, wherein the beneficial bacteria areencapsulated and are administered orally.
 13. The method of claim 8,wherein the population of beneficial bacteria are selected from thegroup consisting of Coprococcus, Roseburia, Bifidobacterium, andFaecalibacterium prausnitzii.
 14. A method for reducing the likelihoodof developing osteoporosis in an individual, comprising: orallyproviding to an individual beneficial bacteria comprising bifidobacteriaand Faecalibacterium prausnitzii, wherein said beneficial bacteria areencapsulated in a shell that protects said beneficial bacteria fromcontact with an individual’s stomach acid; administering fiber to theindividual to maintain a therapeutically effective amount of thebeneficial bacteria in the gut of the individual; wherein saidbeneficial bacteria are effective to modulate the individual’s gutmicrobiome in a manner that reduces osteoporosis.
 15. The method ofclaim 14, further comprising administering at least one of tomatidineand rapamycin to the individual using a bioadhesive strip that has afirst and second side, the second side having a bioadhesive that isadapted to bind to a mucosal membrane for at least 1 hour while inside aperson’s mouth, said strip including at least one polymer selected fromthe group consisting of pullulan, hydroxypropylmethyl cellulose,hydroxyethyl cellulose, sodium alginate, polyethylene glycol, tragacanthgum, guar gum, acacia gum, arabic gum, carboxyvinyl polymer, amylose,high amylose starch, hydroxypropylated high amylose starch, dextrin,chitin, chitosan, levan, elsinan, collagen, zein, gluten, soy proteinisolate, whey protein isolate, casein and mixtures thereof.
 16. Themethod of claim 14, further comprising reducing bacteria in the gut ofthe human being, wherein the bacteria reduced are selected from thegroup consisting of Pediococcus, Streptococcus, Enterococcus, andLeuconostoc bacteria.
 17. The method of claim 16, wherein the step ofreducing the number of bacteria comprises administering an antibiotic.18. The method as set forth in claim 14, further comprisingadministering between 500 mg and 1000 mg of tributyrin to theindividual.
 19. The method as set forth in claim 14, wherein theindividual is a postmenopausal woman.
 20. The method as set forth inclaim 14, further comprising reducing the number of bacteria in theindividual using one of an antibiotic, a clustered regularly interspacedshort palindromic repeats (CRISPR) CRISPR associated protein (Cas)system or a CRISPR from Prevotella and Francisella 1 (Cpf1) system.